bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lattice models in ecology and social sciences
Authors: Nakamaru Mayuko 
Published: March 2006

AbstractRandom matching between individuals, or the complete‐mixing model, is often assumed in analyzing evolutionary or population dynamics in ecology and game theory or other models in social sciences. Making and analyzing a model is not difficult under this simple assumption. However spatial‐ or network‐structured populations, including the lattice model and the power‐law network, are more realistic for many ecological and social phenomena than the complete‐mixing model. In this review, I will show first that a lattice model can be useful in investigating the effect of neighborhood interactions on the dynamics, not only of plants and forests, but also of animal and human societies. Second, the lattice model promotes the evolution of spiteful behavior, even though it is well‐known that the lattice model promotes the evolution of cooperation. Finally, different social networks result in traits, such as social norms, spreading at different speeds.
Indicators of the health of the North Sea fish community: identifying reference levels for an ecosystem approach to management
Authors: Greenstreet Simon P.R. , Rogers Stuart I. 
Published: March 2006

AbstractThe shift in emphasis away from the single-species focus of traditional fisheries management towards an ecosystem approach to management requires application of indicators of ecosystem state. Further, an ecosystem approach to management requires the identification of ecological reference points against which management objectives might be set. In applying indicators, identifying reference points, and setting objectives, an obvious requirement is that the indicators respond primarily to the anthropogenic activity being managed and are sufficiently sensitive that impacts of the activity and the responses to management action are clearly demonstrable. Here we apply a suite of 12 indicators to Scottish August groundfish survey data collected in the northern North Sea over the period 1925–1997. These include indicators of size structure, life-history character composition, species diversity, and trophic structure within the community. Our choice of analytical design has two purposes; first to show that fishing has unequivocally affected these various aspects of the structure of the groundfish community, and second to illustrate an approach by which long time-series data sets might be used to identify possible management reference points. The results are discussed in the context of selecting ecological indicators in support of an ecosystem approach to management and determining appropriate reference points for objective-setting.
Systematic review of topical antimicrobial therapy for acute otitis externa
Authors: Rosenfeld Richard M. , Singer Michael , Wasserman Jared M. , Stinnett Sandra S. 
Published: April 2006

OBJECTIVE: To determine the efficacy of topical antimicrobials for acute otitis externa.STUDY DESIGN: Systematic review and random effects metaanalysis of randomized, controlled trials with parallel groups permitting one or more of the following comparisons: antimicrobial vs placebo, antiseptic vs antimicrobial, quinolone antibiotic vs nonquinolone antibiotic, steroid‐antimicrobial vs antimicrobial, or antimicrobial‐steroid vs steroid.RESULTS: Twenty trials met inclusion criteria and 18 had data suitable for pooling. Topical antimicrobials increased absolute clinical cure rates over placebo by 46% (95% confidence interval [CI], 29% to 63%) and bacteriologic cure rates by 61% (95% CI, 46% to 76%). No significant differences were noted in clinical cure rates for other comparisons, except that steroid alone increased cure rates by 20% compared with steroid plus antibiotic (95% CI, 3% to 38%). Quinolone drops increased bacteriologic cure rates by 8% compared with nonquinolone antibiotics (95% CI, 1% to 16%), but had statistically equivalent rates of clinical cure and adverse eventsCONCLUSION: Topical antimicrobial is highly effective for acute otitis externa with clinical cure rates of 65% to 80% within 10 days of therapy. Minor differences were noted in comparative efficacy, but broad confidence limits containing small effect sizes make these of questionable clinical significance.SIGNIFICANCE: Summary estimates from the 13 meta‐analyses can be used to facilitate evidence‐based management recommendations and clinical practice guideline development. © 2006 American Academy of Otolaryngology‐Head and Neck Surgery Foundation, Inc. All rights reserved.
The Bradford bone-anchored hearing aid programme: impact of the multidisciplinary team
Authors: Goodyear P W A , Raine C H , Firth A L , Tucker A G , Hawkins K 
Published: March 2006

Objectives: The aim of this study was to assess the impact on implant survival, abutment skin reaction and patient satisfaction in patients implanted with a bone-anchored hearing aid (BAHA), following the introduction of a multidisciplinary team (MDT) in 1997.Design and methods: Part prospective and retrospective analysis. Implant survival and cause of failures were recorded along with abutment skin reaction (graded as none, mild, moderate and severe, according to the amount of wound care required). Patient satisfaction and quality of life were assessed using a questionnaire enquiring about several aspects of the use and benefits of their BAHA.Setting and participants: Eighty patients treated at the Bradford Royal Infirmary between 1991 and 2005. The unit is a recognized tertiary referral centre.Results and conclusions: Twelve out of 80 implants failed, giving an overall failure rate of 15 per cent. Kaplan–Meier survival curves show a steady decrease in implant survival. The MDT had a positive effect on implant survival and adverse skin reactions, with a higher proportion of patients experiencing no reaction after its introduction. There was a 92.5 per cent response rate to the questionnaire. Overall patient satisfaction was high, both before and after the introduction of the MDT.
Validation of sonotubometry in healthy adults
Authors: van der Avoort S J C , Heerbeek N van , Zielhuis G A , Cremers C W R J 
Published: March 2006

Background: Frequent active opening of the eustachian tube (ET) allows ventilation of the middle ear and equilibration of pressure changes. Active opening is accomplished by the contraction of the paratubal muscles during swallowing. Because a disturbance of the ventilatory function of the ET may contribute to the development of otitis media with effusion, it is important to investigate ET function. Sonotubometry can be used to detect whether the ET can open or not during swallowing acts.Methods: We developed a sonotubometer to test ET ventilatory function in 36 healthy adults. The width of the test signal frequency was between 5500 and 8500 Hz (centre frequency of 7000 Hz) and the loudness was 95 dB. To test reproducibility, testing took place in two sessions of 10 swallowing acts each.Results: Opening of the ET could be registered in 91.6 per cent of the subjects in at least one of the two measurements. The first and the second measurements were highly correlated, with a Spearman's coefficient of 0.907.Conclusion: We confirmed that there is generally a good ventilatory ET function in otologically healthy adults, although, in a few cases, ET opening was not registered. Furthermore, we confirmed that our sonometric test equipment had acceptable reproducibility. Sonotubometry is a promising method for assessing ventilatory ET function. Research is ongoing to test the discriminative power of sonotubometry in children with various otological conditions.
Thyroid hemiagenesis: clinical significance in the patient with thyroid nodule
Authors: Park I-H , Kwon S-Y , Jung K-Y , Woo J-S 
Published: March 2006

Thyroid hemiagenesis is a rare abnormality in which one thyroid lobe fails to develop. Most of the patients diagnosed have an associated thyroid disease. We report the case of a 32-year-old woman who presented with a left thyroid mass which had been gradually increasing in size over a period of two years. A thyroid scan revealed the absence of the right thyroid lobe and isthmus, and a hypoactive nodule was evident in the lower pole of the left lobe. Ultrasonography confirmed the right lobe and the isthmus agenesis. The operative findings confirmed hemiagenesis of the right lobe and nodular hyperplasia in the left lobe.The purpose of this report is to present a patient with hemiagenesis of the thyroid gland who concomitantly had nodular hyperplasia; we also stress the importance of pre-operative differentiation between benign lesions and malignancy in order to aid critical decision making and to facilitate preservation of thyroid function if possible.
Influence of diabetes mellitus on deep neck infection
Authors: Lin H-T , Tsai C-S S , Chen Y-L , Liang J-G 
Published: March 2006

Objective: To investigate the influence of hyperglycaemia on deep neck infection (DNI) and the differences between the diabetic and non-diabetic form of DNI.Study design and setting: Retrospective review of 131 patients with DNI treated between 1993 and 2002 at Shin Kong Memorial Hospital, Taipei, Taiwan.Results: Deep neck infection was significantly more prevalent in patients with diabetes mellitus (DM) over 60 years of age than in non-DM subjects of a similar age (p = 0.004). In the DM group, Klebsiella pneumoniae was the most common aerobic pathogen and tended to involve more than two anatomical spaces (p < 0.0001). Seventeen out of 18 patients (94.4 per cent) displayed an elevated (≥7 per cent) glycosylated haemoglobin level. The DM group had a significantly higher complication rate, longer hospital stay and tracheotomy rate than the non-DM group.Conclusions: Diabetic DNI differs from non-diabetic DNI in several aspects and is associated with a higher morbidity. A greater than normal haemoglobin A1c level was commonly observed.
Suicide in Hong Kong: a case-control psychological autopsy study
Authors: CHEN ERIC Y. H. , CHAN WINCY S. C. , WONG PAUL W. C. , CHAN SANDRA S. M. , CHAN CECILIA L. W. , LAW Y. W. , BEH PHILIP S. L. , CHAN K. K. , CHENG JOANNE W. Y. , LIU KA Y. , YIP PAUL S. F. 
Published: March 2006

Background. The relative contribution of psychosocial and clinical risk factors to suicide among Chinese populations is an important issue. In Hong Kong, this issue requires vigorous examination in light of a 50% increase in suicide rate between 1997 and 2003.Method. Using a case-control psychological autopsy method, 150 suicide deceased were compared with 150 living controls matched by age and gender. Semi-structured interviews were conducted with the next-of-kin of the subjects. Data were collected on a wide range of potential risk and protective factors, including demographic, life event, clinical and psychological variables. The relative contribution of these factors towards suicide was examined in a multiple logistic regression model.Results. Six factors were found to significantly and independently contribute to suicide: unemployment, indebtedness, being single, social support, psychiatric illness, and history of past attempts.Conclusions. Both psychosocial and clinical factors are important in suicides in Hong Kong. They seem to have mediated suicide risk independently. In addition, socio-economic adversities seem to have played a relatively important role in the increasing suicide rate in Hong Kong.
Autobiographical memories and views of the future: In relation to dysphoria
Authors: Dickson Joanne M. , Bates Glen W. 
Published: March 2006

The present study investigated dysphoric individuals' self‐referential processing of autobiographical memories and future personal events, in relation to specificity and response latency. Dysphoric individuals (n = 17) and nondysphoric controls (n = 17) were selected from a larger sample based on self‐reported depression. Participants completed an autobiographical memory task (AMT) and a future event task (FET), using pleasant and unpleasant (anxiety‐relevant, depression‐relevant) emotional word cues. In response to each emotional cue, participants were required to access and write down a specific personal memory and future event, respectively. Consistent with the hypotheses, dysphoric individuals were less specific in describing pleasant and unpleasant experiences (particularly pleasant), irrespective of time condition. As expected, dysphoric individuals' specificity for distinct depression‐relevant and anxiety‐relevant experiences did not differ significantly. As predicted, all participants were less specific in describing future personal events than in recalling personal memories. As predicted, dysphoric individuals took longer to think of pleasant memories and pleasant future experiences than controls but, as expected, groups did not differ significantly on mean reaction times for past and future unpleasant experiences. Overall, the data showed a degree of consistency in participants' past and future‐oriented processing of self‐referential material. Although considerable research has investigated autobiographical memories in relation to emotional disturbance, the present findings suggest that constructing future emotional experiences is also an important aspect of mental health.
Benchmarking scientific journals from the submitting author's viewpoint
Authors: Björk Bo‐Christer , Holmström Jonas 
Published: April 2006

ABSTRACTAuthors of scholarly papers to a large extent base the decision on where to submit their manuscripts on the prestige of journals, taking little account of other possible factors. Information concerning such factors is in fact often not available. This paper argues for the establishment of methods for benchmarking scientific journals, taking into account a wider range of journal performance parameters than is currently available. A model for how prospective authors determine the value of submitting to a particular journal is presented. The model includes eight factors that influence an author's decision and 21 other underlying factors. The model is a qualitative one. The method proposes to benchmark groups of journals by application of the factors. Initial testing of the method has been undertaken in one discipline.
A structure theorem for the elementary unimodular vector group
Authors: Jose Selby , Rao Ravi 
Published: March 2006

Given a pair of vectors

v
,
w
∈

R

r
+
1

v,w\in R^{r+1}

with

⟨
v
,
w
⟩
=
v
⋅

w
T

=
1

\langle v,w\rangle =v\cdot w^T=1

, A. Suslin constructed a matrix

S
r

(
v
,
w
)
∈
S

l

2
r

(
R
)

S_r(v,w)\in Sl_{2^r}(R)

. We study the subgroup

S
U

m
r

(
R
)

SUm_r(R)

generated by these matrices, and its (elementary) subgroup

E
U

m
r

(
R
)

EUm_r(R)

generated by the matrices

S
r

(

e
1

ε
,

e
1

ε

T

−
1

)

S_r(e_1\varepsilon ,e_1\varepsilon ^{T^{-1}})

, for

ε
∈

E

r
+
1

(
R
)

\varepsilon \in E_{r+1}(R)

. The basic calculus for

E
U

m
r

(
R
)

EUm_r(R)

is developed via a key lemma, and a fundamental property of Suslin matrices is derived.
SScore: an R package for detecting differential gene expression without gene expression summaries
Authors: Kennedy Richard E. , Kerns Robnet T. , Kong Xiangrong , Archer Kellie J. , Miles Michael F. 
Published: March 2006

Abstract
Summary: SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without requiring a preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with the expression summary estimation process and has been demonstrated to improve the accuracy of identifying differentially expressed genes. The S-score produces accurate results even when few or no replicates are available.
Availability: The R package SScore is available from Bioconductor at
Contact: rkennedy@vcu.edu
SBMLToolbox: an SBML toolbox for MATLAB users
Authors: Keating Sarah M. , Bornstein Benjamin J. , Finney Andrew , Hucka Michael 
Published: March 2006

Abstract
Summary: We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML.
Availability: SBMLToolbox is freely available from
Contact: s.m.keating@herts.ac.uk
PseudoPipe: an automated pseudogene identification pipeline
Authors: Zhang Zhaolei , Carriero Nicholas , Zheng Deyou , Karro John , Harrison Paul M. , Gerstein Mark 
Published: March 2006

Abstract
Motivation: Mammalian genomes contain many ‘genomic fossils’ i.e. pseudogenes. These are disabled copies of functional genes that have been retained in the genome by gene duplication or retrotransposition events. Pseudogenes are important resources in understanding the evolutionary history of genes and genomes.
Results: We have developed a homology-based computational pipeline (‘PseudoPipe’) that can search a mammalian genome and identify pseudogene sequences in a comprehensive and consistent manner. The key steps in the pipeline involve using BLAST to rapidly cross-reference potential “parent” proteins against the intergenic regions of the genome and then processing the resulting “raw hits” -- i.e. eliminating redundant ones, clustering together neighbors, and associating and aligning clusters with a unique parent. Finally, pseudogenes are classified based on a combination of criteria including homology, intron-exon structure, and existence of stop codons and frameshifts.
Availability: The PseudoPipe program is implemented in Python and can be downloaded at
Contact: Mark.Gerstein@yale.edu or zhaolei.zhang@utoronto.ca
Mathematical models in physiology
Authors: Gavaghan David , Garny Alan , Maini Philip K , Kohl Peter 
Published: March 2006

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (
modelling OR modeling
) yields over 58 000 entries in PubMed, with more than 34 000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5–6 years, compared to only about one-third in the preceding 5–6 decades.

The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function—the Physiome.
The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations.
Endogenous driving and synchronization in cardiac and uterine virtual tissues: bifurcations and local coupling
Authors: Benson Alan P , Clayton Richard H , Holden Arun V , Kharche Sanjay , Tong Wing C 
Published: March 2006

Cardiac and uterine muscle cells and tissue can be either autorhythmic or excitable. These behaviours exchange stability at bifurcations produced by changes in parameters, which if spatially localized can produce an ectopic pacemaking focus. The effects of these parameters on cell dynamics have been identified and quantified using continuation algorithms and by numerical solutions of virtual cells. The ability of a compact pacemaker to drive the surrounding excitable tissues depends on both the size of the pacemaker and the strength of electrotonic coupling between cells within, between, and outside the pacemaking region.
We investigate an ectopic pacemaker surrounded by normal excitable tissue. Cell–cell coupling is simulated by the diffusion coefficient for voltage. For uniformly coupled tissues, the behaviour of the hybrid tissue can take one of the three forms: (i) the surrounding tissue electrotonically suppresses the pacemaker; (ii) depressed rate oscillatory activity in the pacemaker but no propagation; and (iii) pacemaker driving propagations into the excitable region.
However, real tissues are heterogeneous with spatial changes in cell–cell coupling. In the gravid uterus during early pregnancy, cells are weakly coupled, with the cell–cell coupling increasing during late pregnancy, allowing synchronous contractions during labour. These effects are investigated for a caricature uterine tissue by allowing both excitability and diffusion coefficient to vary stochastically with space, and for cardiac tissues by spatial gradients in the diffusion coefficient.
Reproductive health of Gulf War veterans
Authors: Doyle Patricia , Maconochie Noreen , Ryan Margaret 
Published: March 2006

In this review we summarize the scientific literature on reproductive health following deployment to the first Gulf war by armed service personnel. All the studies examined had methodological limitations, making interpretation difficult. Nonetheless we conclude that for male veterans there is no strong or consistent evidence to date for an effect of service in the first Gulf war on the risk of major, clearly defined, birth defects or stillbirth in offspring conceived after deployment. Effects on specific rare defects cannot be excluded at this stage since none of the studies had the statistical power to examine them. For miscarriage and infertility, there is some evidence of small increased risks associated with service, but the role of bias is likely to be strong. For female veterans, there is insufficient information to make robust conclusions, although the weight of evidence to date does not indicate any major problem associated specifically with deployment to the Gulf. None of the studies have been able to examine risk according particular exposures, and so possible associations with specific exposures for smaller groups of exposed veterans cannot be excluded.
We suggest that the way forward to address the question of veterans' reproductive health with confidence in the future is prospective surveillance following deployment. Anything less will result in further problems of interpretation and continued anxiety for parents, as well as prospective parents, in the armed forces.