bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of large-scale rule-based models
Authors: Colvin Joshua , Monine Michael I. , Faeder James R. , Hlavacek William S. , Von Hoff Daniel D. , Posner Richard G. 
Published: February 2009

AbstractMotivation: Interactions of molecules, such as signaling proteins, with multiple binding sites and/or multiple sites of post-translational covalent modification can be modeled using reaction rules. Rules comprehensively, but implicitly, define the individual chemical species and reactions that molecular interactions can potentially generate. Although rules can be automatically processed to define a biochemical reaction network, the network implied by a set of rules is often too large to generate completely or to simulate using conventional procedures. To address this problem, we present DYNSTOC, a general-purpose tool for simulating rule-based models.Results: DYNSTOC implements a null-event algorithm for simulating chemical reactions in a homogenous reaction compartment. The simulation method does not require that a reaction network be specified explicitly in advance, but rather takes advantage of the availability of the reaction rules in a rule-based specification of a network to determine if a randomly selected set of molecular components participates in a reaction during a time step. DYNSTOC reads reaction rules written in the BioNetGen language which is useful for modeling protein–protein interactions involved in signal transduction. The method of DYNSTOC is closely related to that of StochSim. DYNSTOC differs from StochSim by allowing for model specification in terms of BNGL, which extends the range of protein complexes that can be considered in a model. DYNSTOC enables the simulation of rule-based models that cannot be simulated by conventional methods. We demonstrate the ability of DYNSTOC to simulate models accounting for multisite phosphorylation and multivalent binding processes that are characterized by large numbers of reactions.Availability: DYNSTOC is free for non-commercial use. The C source code, supporting documentation and example input files are available at http://public.tgen.org/dynstoc/.Contact: dynstoc@tgen.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information
Authors: Tong Joo Chuan , Lim Shen Jean , Muh Hon Cheng , Chew Fook Tim , Tammi Martti T. 
Published: February 2009

Abstract
Summary: A variety of specialist databases have been developed to facilitate the study of allergens. However, these databases either contain different subsets of allergen data or are deficient in tools for assessing potential allergenicity of proteins. Here, we describe Allergen Atlas, a comprehensive repository of experimentally validated allergen sequences collected from in-house laboratory, online data submission, literature reports and all existing general-purpose and specialist databases. Each entry was manually verified, classified and hyperlinked to major databases including Swiss-Prot, Protein Data Bank (PDB), Gene Ontology (GO), Pfam and PubMed. The database is integrated with analysis tools that include: (i) keyword search, (ii) BLAST, (iii) position-specific iterative BLAST (PSI-BLAST), (iv) FAO/WHO criteria search, (v) graphical representation of allergen information network and (vi) online data submission. The latest version contains information of 1593 allergen sequences (496 IUIS allergens, 978 experimentally verified allergens and 119 new sequences), 56 IgE epitope sequences, 679 links to PDB structures and 155 links to Pfam domains.
Availability: Allergen Atlas is freely available at http://tiger.dbs.nus.edu.sg/ATLAS/.
Contact: martti@nus.edu.sg.
A Bayesian approach to estimating target strength
Authors: Fässler Sascha M. M. , Brierley Andrew S. , Fernandes Paul G. 
Published: February 2009

Abstract
Fässler, S. M. M., Brierley, A. S., and Fernandes, P. G. 2009. A Bayesian approach to estimating target strength. – ICES Journal of Marine Science, 66: 1197–1204. Currently, conventional models of target strength (TS) vs. fish length, based on empirical measurements, are used to estimate fish density from integrated acoustic data. These models estimate a mean TS, averaged over variables that modulate fish TS (tilt angle, physiology, and morphology); they do not include information about the uncertainty of the mean TS, which could be propagated through to estimates of fish abundance. We use Bayesian methods, together with theoretical TS models and in situ TS data, to determine the uncertainty in TS estimates of Atlantic herring (Clupea harengus). Priors for model parameters (surface swimbladder volume, tilt angle, and s.d. of the mean TS) were used to estimate posterior parameter distributions and subsequently build a probabilistic TS model. The sensitivity of herring abundance estimates to variation in the Bayesian TS model was also evaluated. The abundance of North Sea herring from the area covered by the Scottish acoustic survey component was estimated using both the conventional TS–length formula (5.34×109 fish) and the Bayesian TS model (mean = 3.17×109 fish): this difference was probably because of the particular scattering model employed and the data used in the Bayesian model. The study demonstrates the relative importance of potential bias and precision of TS estimation and how the latter can be so much less important than the former.
Acoustic estimates of mesopelagic fish: as clear as day and night?
Authors: O'Driscoll Richard L. , Gauthier Stéphane , Devine Jennifer A. 
Published: February 2009

Abstract
O'Driscoll, R. L., Gauthier, S., and Devine, J. A. 2009. Acoustic estimates of mesopelagic fish: as clear as day and night? – ICES Journal of Marine Science, 66: 1310–1317. The pelagic ecosystem on the Chatham Rise east of New Zealand has been monitored annually using acoustic surveys since 2001. Most of the acoustic backscatter comes from diurnally migrating mesopelagic fish, which are the major prey of hoki (Macruronus novaezelandiae) and other valuable commercial species. Mesopelagic schools and layers typically occur at 100–400 m depth during the day and migrate above 200 m depth at night. Previous acoustic estimates of the biomass of mesopelagic fish on the Chatham Rise were based only on night-time estimates from the upper 200 m and may significantly underestimate actual biomass. Paired day–night comparisons found that an estimated 20% of the total daytime backscatter migrates to depths of 0–14 m at night, where it is too shallow to be detected by hull-mounted acoustic instruments. In contrast, there is a positive bias associated with acoustic estimates of mesopelagic organisms during the day because they can occur close to the bottom mixed with demersal fish. Two alternative approaches for estimating biomass of diurnally migrating mesopelagic species are suggested. The first applies a correction based on the estimated proportion of backscatter migrating into the surface deadzone to night-time estimates of backscatter in the upper 200 m. The second uses night-time estimates of demersal backscatter, which remains deeper than 200 m at night, to correct daytime estimates of total backscatter. Both methods gave similar estimates of abundance and demonstrated that there was no statistically significant trend in mesopelagic fish biomass on the Chatham Rise over the past seven years.
Clinical trial: factors associated with resolution of heartburn in patients with reflux oesophagitis – results from the EXPO study
Authors: LABENZ J. , ARMSTRONG D. , ZETTERSTRAND S. , EKLUND S. , LEODOLTER A. 
Published: February 2009

SummaryBackground  The ability to predict symptom response to reflux oesophagitis‐healing therapy may optimize treatment decisions.Aim  To identify factors associated with heartburn resolution in patients receiving acid‐suppressive therapy for reflux oesophagitis.Methods  In this multicentre, randomized, double‐blind trial (EXPO; AstraZeneca study code: SH‐NEG‐0008), patients with endoscopically confirmed reflux oesophagitis and reflux symptoms received once‐daily proton pump inhibitor therapy [esomeprazole 40 mg (n = 1562) or pantoprazole 40 mg (n = 1589)] for ≥4 weeks. Factors associated with heartburn resolution after 4 weeks were identified by multiple logistic regression analysis.Results  Esomeprazole therapy, positive Helicobacter pylori status and greater age were associated with an increased likelihood of heartburn resolution [odds ratio (95% confidence interval): 1.31 (1.12, 1.54), 1.44 (1.19, 1.74) and 1.013 (1.007, 1.019) per year, respectively; all P < 0.001]. Men and patients with no acid regurgitation or epigastric pain pre‐treatment were also more likely to achieve heartburn resolution (all P < 0.05).Conclusions  The use of esomeprazole rather than pantoprazole increases the probability of achieving resolution of heartburn during reflux oesophagitis‐healing therapy. Other factors, including H. pylori status, age, gender and symptom profile may be helpful in determining the likelihood of heartburn resolution in such patients.
Insights into syndepositional fault movement in a foreland basin; trends in seismites of the Upper Cretaceous, Wahweap Formation, Kaiparowits Basin, Utah, USA
Authors: Hilbert‐Wolf Hannah L. , Simpson Edward L. , Simpson Wendy S. , Tindall Sarah E. , Wizevich Michael C. 
Published: February 2009

ABSTRACTThe Upper Cretaceous Wahweap Formation accumulated in the active Cordilleran foreland basin of Utah. Soft‐sediment deformation structures are abundant in the capping sandstone member of the Wahweap Formation. By comparing with well‐established criteria, a seismogenic origin was determined for the majority of structures, which places these soft‐sediment deformation features in a class of sedimentary features referred to as seismites. A systematic study of the seismite trends included their vertical and horizontal distribution and a semi‐quantitative intensity analysis using a scale from 1 to 5 that is based on magnitude, sedimentary structure type, and the predominance of inferred process of hydroplastic deformation, liquefaction or fluidization. In addition, orientations of soft‐sediment fold axes were recorded. Construction of a northwest‐to‐southeast stratigraphic and seismite intensity cross‐section demonstrates: (1) reduction in stratigraphic thickness and percentage of conglomerates to the southeast, (2) the presence of lower seismite, middle nonseismite, and upper seismite zones within the capping sandstone (permitting subdivision of the capping sandstone member), and (3) elimination of the nonseismite zone and amalgamation of the lower and upper seismite zones to the southeast. Regional isoseismal contour maps generated from the semi‐quantitative analysis indicate a decrease in overall intensity from northwest to southeast in the upper and lower seismic zones and in sandstone within 5 m stratigraphically of the contact between the upper and capping sandstone members. In addition, cumulative seismite fold orientations support a west–northwest direction towards regional epicentres. Isoseismal maps are used to distinguish the effects of intrabasinal normal faulting from those of regional orogenic thrusting. Thus, this study demonstrates the utility of mapping seismites to separate the importance of regional vs. local tectonic activity influencing foreland basin sedimentation by identifying patterns that delineate palaeoepicentres associated with specific local intrabasinal normal faults vs. regional trends in soft‐sediment deformation related to Sevier belt earthquakes.
The production of JAK2 wild‐type platelets is not downregulated in patients with JAK2 V617F mutant‐positive essential thrombocythaemia
Authors: Lambert Jonathan R. , Gale Rosemary E. , Linch David C. 
Published: February 2009

SummaryTo clarify the relationship between the levels of JAK2 wild‐type (WT) and V617F mutant‐positive platelets in patients with essential thrombocythaemia (ET), we quantified mutant levels in purified cells from 10 V617F‐positive patients prior to receiving cytoreductive therapy. Mutant levels were significantly higher in platelet than neutrophil RNA (P = 0·002), but the mutation was still only present in a sub‐population of platelets (median 54%). When the absolute number of WT platelets was calculated, it was always within or above the normal platelet range, indicating that there is an aberration in the negative feedback to JAK2 WT platelets in ET.
Effect of educational intervention on adoption of new endodontic technology by general dental practitioners: a questionnaire survey
Authors: Koch M. , Eriksson H. G. , Axelsson S. , Tegelberg Å. 
Published: February 2009

AbstractObjectives  To survey the clinical endodontic protocols of general dental practitioners (GDPs) in public dental clinics and to assess the effect of an educational intervention on the adoption of a nickel–titanium (Ni–Ti) rotary system.Methods  General dental practitioners in a Swedish Intervention County (IC), underwent an educational programme in endodontics. A follow‐up questionnaire was posted to 98 GDPs in the IC and to 97 GDPs in a Control County (CC), where no specific training had been provided. The questionnaire concerned demographics, clinical endodontic protocols and instrumentation techniques.Results  The response rate to the questionnaire was 87%. More than 90% of all GDPs reported they always or generally used rubber dam, determined working length, used the canal irrigant 0.5% buffered NaOCl and calcium hydroxide as an interappointment dressing. Two of three GDPs reported, they generally or always informed the patient of the prognosis. Every second GDP reported routines for postoperative recall and follow‐up.The Ni–Ti rotary technique was reported to be completely adopted by 77% of the GDPs in the IC, significantly higher than in the CC (6%), P < 0.001. In the IC 79% of the GDPs reported they completed instrumentation in one treatment session, compared with only 32% in the CC, P < 0.001. The ‘single‐cone’ mode of canal filling was reported to be significantly more frequent amongst GDPs in the IC, P < 0.001.Conclusions  General dental practitioners in both counties reported using contemporary clinical endodontic protocols. GDPs who had undergone an educational programme in Ni–Ti rotary instrumentation reported they had successfully integrated the technique into daily clinical practice.
Quality of life after microscopic periradicular surgery using two different incision techniques: a randomized clinical study
Authors: Del Fabbro M. , Taschieri S. , Weinstein R. 
Published: February 2009

AbstractAim  To monitor the quality of life of patients after periradicular surgery when two different flap designs were used.Methodology  Forty patients with teeth having a periradicular lesion of endodontic origin were included according to specific selection criteria. Patients were randomly assigned to two groups. In one group a sulcular incision (SI) with complete papilla mobilization was made, and in the other group a papilla‐base incision (PBI) was used. Periradicular surgery was performed using a surgical microscope. Parameters related to life quality were recorded daily in the first week post‐surgery using a questionnaire. Pain was evaluated with a 0–100 visual analog scale (VAS). Other symptoms (swelling, bleeding and nausea), plus functions (chewing, speaking, sleeping, daily routine and work) were assessed using a five‐point scale. Analgesic intake was recorded. Fisher’s test and unpaired t‐test were used to assess the difference between groups.Results  The VAS score for pain, and the scores for swelling, chewing and phonetic impairment, peaked on days 1 and 2 postoperatively. A significant difference in favour of the PBI group was found for chewing and swelling in the first 4 days. Starting from day 3 post‐surgery, the PBI group reported a significantly more rapid decrease in pain levels and analgesics use than the SI group (P < 0.05). The other parameters were similar in the two groups.Conclusions  The papilla‐base incision technique may be preferred as reduction of pain levels, swelling and drug intake were more rapid in the first week postoperatively compared with cases in which a sulcular incision was used.
The properties and applications of chlorhexidine in endodontics
Authors: Mohammadi Z. , Abbott P. V. 
Published: February 2009

AbstractMicroorganisms and their by‐products are considered to be the major cause of pulp and periradicular pathosis. Hence, a major objective in root canal treatment is to disinfect the entire root canal system, which requires that all contents of the root canal system be eliminated as possible sources of infection. This goal may be accomplished using mechanical instrumentation and chemical irrigation, in conjunction with medication of the root canal system between treatment sessions. To reduce or eliminate bacteria, various irrigation solutions have been advocated. Chlorhexidine is a cationic molecule, which can be used during treatment. It has a wide range of antimicrobial activity. Its cationic structure provides a unique property named substantivity. The purpose of this paper is to review the structure and mechanism of action of CHX, its antibacterial and antifungal activity, its effect on biofilm, its substantivity (residual antibacterial activity), its tissue solvent ability, its interaction with calcium hydroxide and sodium hypochlorite, its anticollagenolytic activity, its effect on coronal and apical leakage of bacteria, its toxicity and allergenicity and the modulating effect of dentine and root canal components on its antimicrobial activity. A Medline search was performed from 1981 to the end of March 2008 and was limited to English‐language papers. The keywords searched on Medline were ‘chlorhexidine AND endodontics’, ‘chlorhexidine AND root canal therapy’, ‘chlorhexidine AND substantivity’ and ‘chlorhexidine AND toxicity’. The reference lists of each article were manually checked for additional articles of relevance.
The development of dentist practice profiles and management
Authors: Lin Chinho , Lin Chun‐Mei , Hong Chienwen 
Published: February 2009

AbstractRationale and objectives  With the current large computerized payment systems and increase in the number of claims, unusual dental practice patterns to cover up fraud are becoming widespread and sophisticated. Clustering the characteristic of dental practice patterns is an essential task for improving the quality of care and cost containment. This study aims at providing an easy, efficient and practical alternative approach to developing patterns of dental practice profiles. This will help the third‐party payer to recognize and describe novel or unusual patterns of dental practice and thus adopt various strategies in order to prevent fraudulent claims and overcharges.Methodology  Knowledge discovery (or data mining) was used to cluster the dentists' profiles by carrying out clustering techniques based on the features of service rates. It is a hybrid of the knowledge discovery, statistical and artificial neural network methodologies that extracts knowledge from the dental claim database.Results  The results of clustering highlight characteristics related to dentists' practice patterns, and the detailed managerial guidance is illustrated to support the third‐party payer in the management of various patterns of dentist practice.Conclusion  This study integrates the development of dentists' practice patterns with the knowledge discovery process. These findings will help the third‐party payer to discriminate the patterns of practice, and also shed more light on the suspicious claims and practice patterns among dentists.
Explaining the national differences in pressure ulcer prevalence between the Netherlands and Germany – adjusted for personal risk factors and institutional quality indicators
Authors: Tannen Antje , Dietz Ekkehart , Dassen Theo , Halfens Ruud 
Published: February 2009

AbstractBackground  Pressure ulcers have a known impact on quality of life as well as on morbidity and mortality of the persons affected. Remarkable differences in pressure ulcer prevalence between the Netherlands and Germany have been found during the last 6 years. This study explores to what extent the individual risk of the population and quality indicators of the institutions can explain the variation in national prevalence.Methods  Data of a binational multi‐centred cross‐sectional study in 103 hospitals (n = 21 378 patients) and 129 nursing homes (n = 15 579 residents) were analysed using random effects regression models to calculate the differences in national prevalences within the nursing homes and hospitals, adjusted for personal risk for pressure ulcer and quality indicators.Results  The prevalence of pressure ulcers among the at‐risk group (Bradenscore ≤20) in nursing homes was 30.8% in the Netherlands and 8.3% in Germany [OR: 4.9 (CI 95%: 4.2–5.7)]. In hospitals, the prevalence among the at‐risk group was 26.1% in the Netherlands and 21.2% in Germany [OR: 1.3 (CI 95%: 1.2–1.5)]. After adjusting for individual risk factors (age, gender, Bradenscore) as well as for quality structures (use of prevention and treatment protocols, experts groups, information leaflets, nurses training, central pressure ulcer statistics and regular updating of protocols), the chance of developing a pressure ulcer was 6.05 times higher (CI 95%: 4.0–9.2) in a Dutch nursing home than in a German nursing home. Within the hospitals, the OR for Dutch patients was 2.03 (CI 95%: 1.4–3.0).Conclusion  A remarkable national variation exists in pressure ulcer prevalence and nursing practice. Neither the populations vulnerability for pressure ulcers nor pressure ulcer management as measured in this study could explain this national variation. Therefore, other risk factors should be taken into consideration. Additionally, it is possible that quality indicators are implemented in differing ways with varying levels of effectiveness. Therefore, further research is needed to examine prospectively and in more detail the reality of care within facilities in both countries.
Secondary care doctors' perception of appropriate prescribing
Authors: Ljungberg Christina , Lindblad Åsa Kettis , Tully Mary 
Published: February 2009

AbstractRationale, aim and objective  As the prescribing of drugs in secondary care is known to influence prescribing in primary care and because an understanding of prescribers' reasoning is essential for evaluating prescribing appropriateness, the aim of this study was to investigate secondary care doctors' views of appropriate prescribing, using qualitative individual interviews.Method  Qualitative, semi‐structured individual interviews were conducted with 15 hospital doctors working in different medical specialities. The interviews, covering the doctors' views of the meaning of ‘appropriate’ prescribing, were audiotaped and analysed from an interpretivist perspective.Results  Three different main themes were identified in the analysis of how the doctors perceived appropriate prescribing: ‘individualization of treatment’, ‘cost’ and ‘time’. Most importantly, treatment should be adjusted to the individual patient, although cost should also be justified. Ongoing medication reviews should be carried out, to adjust to changes in patient‐related factors over time.Conclusions  The hospital doctors brought up continuous review as a necessary part of appropriate prescribing. Thus, from the prescribers' point of view, this time perspective should be explicitly incorporated in definitions of appropriate prescribing, in addition to individualization of treatment and cost considerations.