bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels)
Authors: Rodin Andrei S. , Boerwinkle Eric 
Published: May 2005

AbstractMotivation: The wealth of single nucleotide polymorphism (SNP) data within candidate genes and anticipated across the genome poses enormous analytical problems for studies of genotype-to-phenotype relationships, and modern data mining methods may be particularly well suited to meet the swelling challenges. In this paper, we introduce the method of Belief (Bayesian) networks to the domain of genotype-to-phenotype analyses and provide an example application.Results: A Belief network is a graphical model of a probabilistic nature that represents a joint multivariate probability distribution and reflects conditional independences between variables. Given the data, optimal network topology can be estimated with the assistance of heuristic search algorithms and scoring criteria. Statistical significance of edge strengths can be evaluated using Bayesian methods and bootstrapping. As an example application, the method of Belief networks was applied to 20 SNPs in the apolipoprotein (apo) E gene and plasma apoE levels in a sample of 702 individuals from Jackson, MS. Plasma apoE level was the primary target variable. These analyses indicate that the edge between SNP 4075, coding for the well-known ε2 allele, and plasma apoE level was strong. Belief networks can effectively describe complex uncertain processes and can both learn from data and incorporate prior knowledge.Availability: Various alternative and supplemental networks (not given in the text) as well as source code extensions, are available from the authors.Contact: arodin@uth.tmc.eduSupplementary information: http://bioinformatics.oxfordjournals.org
Resmap: automated representation of macromolecular interfaces as two-dimensional networks
Authors: Swint-Kruse Liskin , Brown Curties S. 
Published: May 2005

Abstract
Summary: To aid detailed comparison of a large number of macromolecular structures, Resmap imports Protein Data Bank files and represents subunit/domain interfaces as two-dimensional networks.
Availability: http://www.kumc.edu/biochemistry/resmap/
Contact: lswint-kruse@kumc.edu
Supplementary information: Default definitions and directions for graphically managing networks are available at the same website.
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)
Authors: Park Daeui , Lee Semin , Bolser Dan , Schroeder Michael , Lappe Michael , Oh Donghoon , Bhak Jong 
Published: May 2005

AbstractMotivation: Many genomes have been completely sequenced. However, detecting and analyzing their protein–protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein–protein interaction rules within and among complete genomes.Results: We confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of 146 species are scale-free networks, and they share a small core network comprising 36 protein families related to indispensable cellular functions. We found two fundamental differences among prokaryotic and eukaryotic interactomes: (1) eukarya had significantly more hub families than archaea and bacteria and (2) certain special hub families determined the topology of the eukaryotic interactomes. Our comparative analysis suggests that a very small number of expansive protein families led to the evolution of interactomes and seemed tohave played a key role in species diversification.Contact: jong@kribb.re.krSupplementary information: http://interactomics.org
Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm
Authors: Gáspári Zoltán , Vlahovicek Kristian , Pongor Sándor 
Published: May 2005

Abstract
Summary: An improved version of the PRIDE (PRobaility of IDEntity) fold prediction algorithm has been developed, based on more solid statistical basis, fast search capabilities and efficient input structure processing. The new algorithm is effective in identifying protein structures at the ‘H’ level of the CATH hierarchy.
Availability: The new algorithm is integrated into the PRIDE2 web servers at http://pride.szbk.u-szeged.hu and http://www.icgeb.org/pride
Contact: pongor@icgeb.org
Supplementary information: Detailed documentation and performance evaluation is available in the description section of the PRIDE2 web server.
A symmetry analysis of mechanisms in rotating rings of tetrahedra
Authors: Fowler P.W , Guest S.D 
Published: May 2005

Rotating rings of tetrahedra are well known from recreational mathematics. Rings of
N
tetrahedra with
N
even are analysed by symmetry-adapted versions of classical counting rules of mechanism analysis. For
N
≥ 6, a single state of self-stress is found, together with
N
−5 symmetry-distinct mechanisms, which include the eponymous rotating mechanism. For
N
=4 in a generic configuration, a single mechanism remains together with three states of self-stress, but, uniquely in this case, the mechanism path passes through a bifurcation at which the number of mechanisms and states of self-stress is raised by one.
Limited genetic exchanges between populations of an insect pest living on uncultivated and related cultivated host plants
Authors: Vialatte Aude , Dedryver Charles-Antoine , Simon Jean-Christophe , Galman Marina , Plantegenest Manuel 
Published: May 2005

Habitats in agroecosystems are ephemeral, and are characterized by frequent disturbances forcing pest species to successively colonize various hosts belonging either to the cultivated or to the uncultivated part of the agricultural landscape. The role of wild habitats as reservoirs or refuges for the aphidSitobion avenaethat colonize cultivated fields was assessed by investigating the genetic structure of populations collected on both cereal crops (wheat, barley and oat) and uncultivated hosts (Yorkshire fog, cocksfoot, bulbous oatgrass and tall oatgrass) in western France.Classical genetic analyses and Bayesian clustering algorithms indicate that genetic differentiation is high between populations collected on uncultivated hosts and on crops, revealing a relatively limited gene flow between the uncultivated margins and the cultivated part of the agroecosystem. A closer genetic relatedness was observed between populations living on plants belonging to the same tribe (Triticeae, Poeae and Aveneae tribes) where aphid genotypes appeared not to be specialized on a single host, but rather using a group of related plant species. Causes of this ecological differentiation and its implications for integrated pest management ofS. avenaeas cereals pest are discussed.
Assessment of gastric volume changes with sonometry compared with barostat
Authors: Ouyang H. , Chen J. D. Z. 
Published: May 2005

Abstract  Aim:  The aim was to investigate the validity of sonometry on the assessment of gastric volumes in comparison with gastric barostat.Method:  Six dogs were implanted with gastric serosal electrodes, sonometric sensors, and a gastric cannula. Experiments were performed to assess sensor distance when an intragastric balloon was inflated with different volumes, after a meal with or without a balloon, and with gastric electrical stimulation.Results:  (i) The distance measured using sonometry was reproducible and stable, and there was a correlation between sensor distance and the gastric volume measured with barostat. (ii) Simultaneous recordings by sonometry and barostat showed a similar postprandial response, while the postprandial increase of the sensor distance was much smaller without the balloon (3.2 ± 0.2 mm vs 9.7 ± 1.5 mm, P < 0.02). (iii) The sensor distance was increased with gastric electrical stimulation.Conclusions:  Sonometry is able to detect gastric volume changes as validated by gastric perturbations with distensions, food ingestion and electrical stimulation. The postprandial increase in gastric volume measured by sonometry with barostat balloon is greater because of the presence of the intragastric balloon.
Disposable balloon‐based oesophageal motility catheters: comparison with solid‐state transducers*
Authors: Tutuian R. , Agrawal A. , Mainie I. , Freeman J. , Castell D. O. 
Published: May 2005

Abstract  Background:  Current oesophageal manometry systems use either water‐perfused or solid‐state pressure transducers. Recently developed single‐use disposable catheters use small balloons prefilled with air that transmit the pressure of oesophageal contractions to external transducers.Aim:  To compare data obtained from single‐use disposable balloon catheters to data from solid‐state systems.Methods:  Healthy volunteers, patients with ineffective oesophageal motility and nutcracker oesophagus were studied to include a broad range of pressures. A single‐use disposable Clinical Innovations (CI) catheter was placed adjacent to a solid‐state Konigsberg Instruments (KI) catheter with pressure transducers at 5, 10, 15 and 20 cm above the lower oesophageal sphincter (LOS). Subjects received liquid and viscous swallows at 30‐s intervals. Healthy volunteers received additional sets of swallows while having only one catheter in the oesophagus.Results:  When both catheters were present in the oesophagus, no differences were noted between mean pressure measurements in the distal oesophagus and there was good correlation between pressures recorded in response to individual swallows. When present alone in the oesophagus the CI catheter recorded lower mean pressures compared with the KI catheter. Overall there was good agreement in classifying swallows as normal, ineffective and simultaneous.Conclusion:  Single‐use oesophageal manometry catheters are promising alternatives to solid‐state manometry systems in measuring intra‐oesophageal pressures.
Reflections of occupational therapists working as members of a research team
Authors: Finlayson Marcia , Shevil Eynat , Mathiowetz Virgil , Matuska Kathleen 
Published: May 2005

Aim:  This qualitative study explored the effects of clinician participation in a randomised clinical trial on subsequent practice. Method:  Eight occupational therapists responded to open‐ended questions delivered by email about their reflections on participating in clinical research and its impact on their practice. Qualitative analysis uncovered therapists’ motivation to participate in research, what they felt that they gained, and if and how research participation influenced practice. Results:  Clinicians learned about research, practice, and their own clinical biases through their participation in clinical research. Conclusion:  Our findings suggest that participation in research may contribute to shrinking the research‐practice gap.
Towards facilitating change in service delivery: An illustrative example
Authors: Boshoff Kobie 
Published: May 2005

Background:  The management of change in organisations is a challenge facing many occupational therapists in practice today. This article presents an example of a program implemented to facilitate the process of change in paediatric service delivery. It presents the principles and design of the program, as well as the program's implementation and resultant findings. Methods:  The principles and process of organisational change laid the foundation of the program and were utilised as measurement of changes occurring in the perceptions of participants. Interviews and online focus groups were utilised as data‐gathering methods. Results:  The findings of the study illustrate the process of change that participants were undergoing. Conclusions:  The article provides an example of how managers can facilitate change in service delivery by using the principles of organisational change and adult learning. Recommendations are made for application of similar change management processes in other organisations and the future use of the online discussion medium as research tool and in practice.
FGF19‐FGFR4 signaling elaborates lens induction with the FGF8‐L‐Maf cascade in the chick embryo
Authors: Kurose Hitomi , Okamoto Mayumi , Shimizu Miyuki , Bito Takaaki , Marcelle Cristophe , Noji Sumihare , Ohuchi Hideyo 
Published: May 2005

The fibroblast growth factor (FGF) family is known to be involved in vertebrate eye development. However, distinct roles of individual FGF members during eye development remain largely elusive. Here, we show a detailed expression pattern of Fgf19 in chick lens development. Fgf19 expression initiated in the forebrain, and then became restricted to the distal portion of the optic vesicle abutting the future lens placode, where FGF receptor 4 (Fgfr4), a receptor for FGF19, was expressed. Fgf8, a positive regulator for L‐Maf, was expressed in a portion of the optic vesicle. To examine the role of FGF19 signaling during early eye development, Fgf19 was misexpressed near the presumptive lens ectoderm; however, no alteration in the expression of lens marker genes was observed. Conversely, a secreted form of FGFR4 was misexpressed to inhibit an FGF19 signal, resulting in the induction of L‐Maf expression. To further define the relationship between L‐Maf and Fgf19, L‐Maf misexpression was performed, resulting in ectopic induction of Fgf19 expression by Hamburger and Hamilton's stage 12/13. Furthermore, misexpression of Fgf8 induced Fgf19 expression in addition to L‐Maf. These results suggest that FGF19‐FGFR4 signaling plays a role in early lens development in collaboration with FGF8 signaling and L‐Maf transcriptional system.
Postnatal changes in the expression of p60c‐Src in mouse testes
Authors: Gye Myung Chan , Choi Jin Kook , Ahn Hyun Soo , Kim Young Soo 
Published: May 2005

Src family non‐receptor tyrosine kinases are involved in signaling pathways which mediate cell growth, differentiation, transformation and tissue remodeling in various organs. In an effort to elucidate functional involvement of p60c‐Src (c‐Src) in spermatogenesis, the postnatal changes in c‐src mRNA and c‐Src protein together with kinase activity and subcellular localization were examined in mouse testes. c‐src mRNA levels in testes increased during the first 2 weeks of postnatal development (PND). Following a decrease at puberty (PND 28), the c‐src mRNA levels re‐increased at adulthood (PND 50). Src kinase activity of testes was low at PND 7 but sharply increased prepubertally (PND 15) and highest at adulthood. Upon Western blotting, the level of c‐Src protein was the highest in prepubertal testes but rather decreased in adult testes at PND 50. In adult testes, ubiquitination of c‐Src proteins was apparent compared with immature one at PND 7, suggesting active turnover of c‐Src by ubiquitination. In immature testes, c‐Src immunoreactivity was largely found in the cytoplasm of the Sertoli cells. By contrast, in pubertal and adult testes intense immunoreactivity was localized at the adluminal and basal cytoplasm of Sertoli cells bearing elongated spermatids and early germ cells, respectively. The immunoreactivity of c‐Src in the Leydig cells was increased during pubertal development, suggesting the functional involvement of c‐Src in differentiated adult Leydig cells. Throughout postnatal development, some spermatogonia and spermatocytes showed intensive c‐Src immunoreactivity compared with other germ cells, suggesting a possible role of c‐Src in germ cell death. Taken together, it is suggested that c‐Src may participate in the remodeling of the seminiferous epithelia and functional differentiation of Leydig cells during the postnatal development of mouse testes.
Perceptions of behaviour and patterns of exclusion: Gypsy Traveller students in English secondary schools
Authors: Derrington Chris 
Published: May 2005

This paper draws on a recent and unique longitudinal study of Gypsy Traveller students in fifteen local education authorities in England. Gypsy Traveller students are less likely to complete secondary education than any other minority ethnic group and it is estimated that up to 12 000 young Travellers in England are not registered at any secondary school. The study tracked a sample of 44 students over a three‐year period, using a multi‐perspective, phenomenological design to explore the complex interplay of attitudes, expectations and relationships that might impact on secondary school engagement and retention. Findings indicate that, although the students’ behaviour was perceived to be good by their primary school teachers, problems began to emerge during the first year at secondary school and twenty‐four pupils had self‐excluded by the age of fourteen. Furthermore, almost one in three of the students in the study were temporarily excluded by their schools on at least one occasion during the study. The research suggests that patterns of resistance to secondary schooling should not be solely attributed to cultural influences. In many cases, parents expressed positive perceptions of their child's school until relationships broke down. Above all, parents and students want assurance that racism will be challenged and dealt with effectively.
Nondaily Hormonal Contraception: Considerations in Contraceptive Choice and Patient Counseling
Authors: Freeman Sarah 
Published: May 2005

PurposeTo review currently available choices for non‐daily hormonal contraception, considering efficacy, safety, patient counseling issues, and appropriate patient selection.Data SourcesWorldwide medical literature and the individual products' prescribing information.ConclusionsPatients and clinicians have many nondaily hormonal contraceptive options available—from Depo‐Provera quarterly injection, which has been available in the United States for over 10 years, to several new entries (Mirena 5‐year intrauterine system, Lunelle monthly injection, NuvaRing monthly intravaginal ring, and Ortho Evra weekly transdermal patch). All these options offer high efficacy and enhanced convenience for many patients over daily oral contraceptives (OCs). Barriers to use of these agents may include patients’ lack of information as well as fear or misconceptions regarding the hormones and methods. All of these can be addressed with adequate patient counseling and open dialogue. The clinician and patient need to be well‐informed regarding these options so that they can work together and identify the best contraceptive fit for the patient—with the ultimate goal being to increase patient satisfaction and adherence and, thus, avoid unintended pregnancy.Implications for PracticeDespite the efficacy of OCs, missed pills are quite common and contribute to unintended pregnancy. Many women in all population categories would benefit from the convenience and reliability of nondaily hormonal contraceptives. The highest efficacy rates with typical use are associated with agents that require minimal user participation (i.e., Depo‐Provera, Mirena).Compared to daily regimens, all nondaily options offer increased convenience and may contribute to improved patient adherence.However, barriers to use may exist.Patient fears regarding use of hormones can be minimized by discussing the long‐term safety of hormonal contraceptives. (The data are predominantly derived from Depo‐Provera and OCs because these agents have been available in the United States and in the rest of the world for much longer than the newer nondaily options.) Patient counseling and appropriate expectations regarding changes in menstrual pattern have been demonstrated to further enhance patient adherence to therapy. Finally, patient lifestyle preferences must be considered. The finding that many women are comfortable with or even prefer amenorrhea, which is associated with options such as Depo‐Provera, highlights how important it is for clinicians to avoid making assumptions about a patient's contraceptive preferences. Rather, clinicians and patients should exchange information through an open dialogue. For the majority of patients, nondaily hormonal contraceptives should be considered and offered as first‐line options.
Identifying the Drug Seeker: The Advanced Practice Nurse's Role in Managing Prescription Drug Abuse
Authors: Gerhardt Annie M. 
Published: May 2005

PurposeTo provide advanced practice nurses (APNs) with a definition of drug‐seeking behaviors, to identify the common signs and symptoms of drug‐seeking behaviors, to furnish tips for managing interactions with and treatment of the drug‐seeking patient, and to describe pre‐scription parameters that will help APNs avoid legal ramifications.Data SourcesA review of the current scientific and clinical literature regarding interaction with and treatment of patients who abuse prescription drugs.ConclusionsA basic understanding of drug‐seeking behaviors and adherence to appropriate procedures for prescribing controlled medications are essential for APNs to maintain their safe prescribing habits; carry on with quality, effective care; and continue the advancement of their profession.Implications for PracticeAs primary care providers, APNs must be aware of the potential complications resulting from interacting with patients who may be seeking prescription drugs for recreational or illicit use, rather than for legitimate reasons.
Down Syndrome With an Unusual Etiology: Case Report and Review
Authors: Pastva Mattie , Corwin Elizabeth J. , Morin Karen 
Published: May 2005

PurposeTo present the genetic etiology of an unusual case of Down syndrome, arising from translocation of chromosome 21 to chromosome 9; to discuss advanced genetic diagnostic techniques, focusing on how pinpointing a specific genetic mistake can influence treatment and outcome;and to review the role of the nurse practitioner (NP) in caring for families of children with Down syndrome.Data SourcesCase report, literature review, and advanced genetic techniques.ConclusionsNPs often answer patient questions regarding genetic abnormalities and risk factors for transmission of genetic errors to offspring. Advanced genetic analysis allows for the diagnosis of unusual causes of common genetic disorders. The ability to identify a specific genetic mistake and to predict the scope of its effect on an individual offers health care providers the opportunity to develop a case‐by‐case plan of care.Implications for PracticeNPs have a responsibility to be informed about the processes involved in the transmission of genetic errors and about the subtleties of various expressions of a genetic disorder. The availability of new genetic‐testing techniques allows NPs to individualize patient care and family teaching.