bluuebunny/crossref_metadata_2025_split huggingface dataset:
FPC Web Tools for Rice, Maize, and Distribution
Authors: Pampanwar Vishal , Engler Friedrich , Hatfield James , Blundy Steve , Gupta Gaurav , Soderlund Carol 
Published: May 2005

Abstract
Many clone-based physical maps have been built with the FingerPrinted Contig (FPC) software, which is written in C and runs locally for fast and flexible analysis. If the maps were viewable only from FPC, they would not be as useful to the whole community since FPC must be installed on the user machine and the database downloaded. Hence, we have created a set of Web tools so users can easily view the FPC data and perform salient queries with standard browsers. This set includes the following four programs: WebFPC, a view of the contigs; WebChrom, the location of the contigs and genetic markers along the chromosome; WebBSS, locating user-supplied sequence on the map; and WebFCmp, comparing fingerprints. For additional FPC support, we have developed an FPC module for BioPerl and an FPC browser using the Generic Model Organism Project (GMOD) genome browser (GBrowse), where the FPC BioPerl module generates the data files for input into GBrowse. This provides an alternative to the WebChrom/WebFPC view. These tools are available to download along with documentation. The tools have been implemented for both the rice (Oryza sativa) and maize (Zea mays) FPC maps, which both contain the locations of clones, markers, genetic markers, and sequenced clone (along with links to sites that contain additional information).
BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case
Authors: Wilkinson Mark , Schoof Heiko , Ernst Rebecca , Haase Dirk 
Published: May 2005

Abstract
The burden of noninteroperability between on-line genomic resources is increasingly the rate-limiting step in large-scale genomic analysis. BioMOBY is a biological Web Service interoperability initiative that began as a retreat of representatives from the model organism database community in September, 2001. Its long-term goal is to provide a simple, extensible platform through which the myriad of on-line biological databases and analytical tools can offer their information and analytical services in a fully automated and interoperable way. Of the two branches of the larger BioMOBY project, the Web Services branch (MOBY-S) has now been deployed over several dozen data sources worldwide, revealing some significant observations about the nature of the integrative biology problem; in particular, that Web Service interoperability in the domain of bioinformatics is, unexpectedly, largely a syntactic rather than a semantic problem. That is to say, interoperability between bioinformatics Web Services can be largely achieved simply by specifying the data structures being passed between the services (syntax) even without rich specification of what those data structures mean (semantics). Thus, one barrier of the integrative problem has been overcome with a surprisingly simple solution. Here, we present a nontechnical overview of the critical components that give rise to the interoperable behaviors seen in MOBY-S and discuss an exemplar case, the PlaNet consortium, where MOBY-S has been deployed to integrate the on-line plant genome databases and analytical services provided by a European consortium of databases and data service providers.
Databases and Information Integration for the Medicago truncatula Genome and Transcriptome
Authors: Cannon Steven B. , Crow John A. , Heuer Michael L. , Wang Xiaohong , Cannon Ethalinda K.S. , Dwan Christopher , Lamblin Anne-Francoise , Vasdewani Jayprakash , Mudge Joann , Cook Andrew , Gish John , Cheung Foo , Kenton Steve , Kunau Timothy M. , Brown Douglas , May Gregory D. , Kim Dongjin , Cook Douglas R. , Roe Bruce A. , Town Chris D. , Young Nevin D. , Retzel Ernest F. 
Published: May 2005

Abstract
An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support the marker-anchored bacterial artificial chromosome (BAC) sequencing strategy. Existing physical and genetic maps and deep BAC-end sequencing help to guide the sequencing effort, while EST databases provide essential resources for genome annotation as well as transcriptome characterization and microarray design. Finished BAC sequences are joined into overlapping sequence assemblies and undergo an automated annotation process that integrates ab initio predictions with EST, protein, and other recognizable features. Because of the sequencing project's international and collaborative nature, data production, storage, and visualization tools are broadly distributed. This paper describes databases and Web resources for the project, which provide support for physical and genetic maps, genome sequence assembly, gene prediction, and integration of EST data. A central project Web site at medicago.org/genome provides access to genome viewers and other resources project-wide, including an Ensembl implementation at medicago.org, physical map and marker resources at mtgenome.ucdavis.edu, and genome viewers at the University of Oklahoma (www.genome.ou.edu), the Institute for Genomic Research (www.tigr.org), and Munich Information for Protein Sequences Center (mips.gsf.de).
Evolutionary Divergence of Monocot and Dicot Methyl-CpG-Binding Domain Proteins
Authors: Springer Nathan M. , Kaeppler Shawn M. 
Published: May 2005

Abstract
The covalent modification of eukaryotic DNA by methylation of the 5′ carbon of cytosine residues is frequently associated with transcriptional silencing. In mammals, a potential mechanism for transducing DNA methylation patterns into altered transcription levels occurs via binding of methyl-CpG-binding domain (MBD) proteins. Mammalian MBD-containing proteins bind specifically to methylated DNA and recruit chromatin-modifying complexes containing histone deacetylase activities. Sequence similarity searches reveal the presence of multiple proteins in plants containing a putative MBD. Outside of the MBD itself, there is no sequence relationship between plant and mammalian MBD proteins. The plant MBD proteins can be divided into eight classes based on sequence similarity and phylogenetic analyses of sequences obtained from two complete genomes (rice [Oryza sativa] and Arabidopsis [Arabidopsis thaliana]) and from maize (Zea mays). Two classes of MBD proteins are only represented in dicot species. The striking divergence of plant and animal MBD-containing proteins is in stark contrast to the amino acid conservation of DNA methyltransferases across plants, animals, and fungi. This observation suggests the possibility that while plants and mammals have retained similar mechanisms for the establishment and maintenance of DNA methylation patterns, they may have evolved distinct mechanisms for the interpretation of these patterns.
Evaluation of simple non‐invasive techniques for assessment of lower extremity arterial disease
Authors: Sahli David , Svensson Maria , Lidgren Joakim , Öjbrandt Kristina , Eriksson Jan W. 
Published: May 2005

SummaryObjective:  To evaluate the reproducibility and precision of three, simple, non‐invasive methods to measure blood pressure (BP) in the lower extremities by comparing reproducibility and sensitivity in finding abnormally low BP between ankle blood pressure (ABP) and toe blood pressure (TBP), by studying the concordance between TBP in toe 1 and 2 and evaluating the pole‐pox method in patients with diabetes and lower extremity arterial disease (LEAD).Subjects and methods:  The BP was measured twice, 1 week apart, in arms and legs in 13 controls and 12 patients with diabetes. ABP was assessed by using a Doppler pen for pulse registration. TBP was obtained by using a small cuff and a pulse oximetry sensor at toe 1 and 2. In eleven patients with diabetes and previously known LEAD ABP was obtained through the pole‐pox method.Results:  No significant difference in reproducibility between absolute BPs and indices (coefficients of variation <9%) was found. A non‐significant improvement with 4–8% in the sensitivity in detecting LEAD was seen when BP indices were used instead of absolute BP. A significant correlation in the variation over time for systemic and TBP (r = 0·34, P = 0·015) and a strong correlation was found between TBP measured at toe 1 and 2, respectively (r = 0·99, P<0·001) was found. TBP measured with pole‐pox method were significantly correlated with measurements made by the ordinary cuff technique (r = 0·75, P<0·001).Conclusions:  The use of TBP and ABP indices instead of absolute BP does not improve the reproducibility but may improve the sensitivity with respect to detection of LEAD, especially in patients with diabetes. The pole‐pox method may be used as an alternative screening method in patients with diabetes and LEAD.
Effects of ventilation on cardiac output determined by inert gas rebreathing
Authors: Damgaard Morten , Norsk Peter 
Published: May 2005

SummaryOne of the most important methodological problems of the foreign gas rebreathing technique is that outcome of the measurements depends on procedural variables such as rebreathing frequency (RF), rebreathing bag volume (Vreb), lung volume at start of rebreathing and intervals between measurements. Therefore, in 10 healthy males we investigated the effects of changes in ventilation pattern on cardiac output (CO) estimated by an N2O‐rebreathing technique. Reducing the rebreathing volume (Vreb) from 1·5 to 1·0 l diminished CO by 0·5 ± 0·2 l min−1, whereas an increase in Vreb from 1·5 to 2·5 l had no effects. CO was 1·0 ± 0·2 l min−1 higher when, rebreathing was performed after a forced expiration than following a normal tidal expiration. Serial determinations of CO required a 3‐min interval between the measurements to avoid effects of recirculation of N2O. Changing RF from 15 to 30 breaths min−1 or adding serial dead space by up to 600 ml did not affect the determination of CO. In conclusion, the rebreathing procedure for determination of CO at rest should be performed following a normal tidal expiration with a rebreathing bag volume of between 1·5 and 2·5 l and with manoeuvres separated by at least 3–5 min. Variations in RF within the physiological range from 15 to 30 breaths min−1 do not affect outcome of the measurements.
Regional blood flow during hyperoxic haemodilution
Authors: Meier Jens , Pape Andreas , Kleen Martin , Hutter Jörg , Kemming Gregor , Habler Oliver 
Published: May 2005

SummaryBackground:  Ventilation with pure oxygen (hyperoxic ventilation, HV) increases arterial oxygen content (CaO2). However HV induces arteriolar constriction and thus potentially affects O2 supply. We therefore investigated the effects of HV on regional blood flow (RBF) and O2 supply of different vital organs during moderate normovolaemic anaemia.Methods:  Twenty‐two anaesthetized dogs were haemodiluted under normoxia (i.e. FiO2 = 0·21) to a target haemoglobin concentration (Hb) of 7 g dl−1 and were subsequently ventilated with pure O2. RBF was determined by use of the radioactive microspheres method in the myocardium, kidney, skeletal muscle, liver, intestine, stomach, and pancreas at Hb = 7 g dl−1 and after subsequent initiation of HV. RBF in proportion to cardiac output (RBFrelative), the variation coefficient of RBF (VC) and regional O2 supply (rDO2) were calculated.Results:  Initiation of HV at Hb = 7·0 ± 0·3 g dl−1 reduced cardiac index (−17%) as well as RBF within the myocardium (−21%), pancreas (−25%), and skeletal muscle (−25%), whereas renal, hepatic, and intestinal RBF remained unchanged. Consequently RBFrelative of the latter organs increased. Heterogeneity of RBF was marginally affected by HV.Conclusion:  The initiation of HV during moderate normovolaemic anaemia (Hb =7 g dl−1) was accompanied by RBF redistribution with preference for renal, hepatic and intestinal O2 supply. Cardiac, pancreatic and muscular O2 supply decreased, however without any critical restriction of organ function.
A short period of apnoea causes a marked increase in coronary flow velocity: a transthoracic pulsed wave Doppler study
Authors: Gan Li‐ming , Hägg Ulrika , Wandt Birger 
Published: May 2005

SummaryCoronary artery flow velocity during a short period of apnoea was investigated by transthoracic Doppler recording in 10 healthy men, aged 24–52. During breath holding for 29 ± 6 s the oxygen saturation in the finger, measured by pulse oxymetry, decreased from 97·5 ± 0·8 to 90·0 ± 3·2% (P<0·001). The maximal coronary blood flow velocity in the left anterior descending artery increased by 62% from 0·26 ± 0·09 to 0·42 ± 0·10 m s−1 and the mean diastolic flow velocity by 47% from 0·19 ± 0·04 to 0·28 ± 0·08 m s−1 (P<0·001). In most subjects the increase of velocity started already after a few seconds of apnoea. Besides theoretical implications the results show that it is very important to be aware of the higher velocity during apnoea in order to avoid misinterpretation when using breath holding during magnetic resonance imaging or Doppler recording of coronary flow.
Effects of lung volume reduction surgery on distribution of ventilation and perfusion
Authors: Moonen Michaela , Xu Jiahua , Johansson Åke , Thylén Anders , Bake Björn 
Published: May 2005

SummaryLung volume reduction surgery (LVRS) results in functional improvements in most patients. The mechanisms behind the improvements are not clear. We hypothesized that reduced inequalities in ventilation to perfusion ratio (V/Q) may be a contributing explanation. Nine patients who underwent LVRS were investigated by ventilation and perfusion scintigrams before and after surgery. In addition, 8 healthy subjects were investigated once. The relative ventilation, perfusion and V/Q were calculated in 1 × 1 cm lung elements. Normal range of the element count‐rate was determined by the corresponding results in the normal subjects. Results of this small study show a significant effect of LVRS on V/Q, with reduction of shunt‐like elements. We conclude that the functional improvement after LVRS to some extent may be explained by decreased V/Q inequality.
Left ventricular involvement in arrhythmogenic right ventricular cardiomyopathy – a scintigraphic and echocardiographic study
Authors: Lindström Lena , Nylander Eva , Larsson Hans , Wranne Bengt 
Published: May 2005

SummaryBackground:  Left ventricular involvement in arrhythmogenic right ventricular cardiomyopathy (ARVC) is a common finding in autopsy studies. In clinical studies using myocardial scintigraphy, MRI and echocardiography, contradictory results have been reported. In this study, we therefore investigated a group of 15 patients with ARVC using thallium‐201 (Tl) single‐photon emission tomography (SPECT) and echocardiography including assessment of mitral annular motion with M‐mode and pulsed tissue Doppler.Methods:  Exercise and rest Tl‐201 SPECT were performed in 15 patients with ARVC. The time from diagnosis of the disease varied from less than 1–16 years. All patients fulfilled the established diagnostic criteria for ARVC. An echocardiographic examination, including assessment of left and right ventricular motion and measurements of the mitral annulus motion with M‐mode and pulsed tissue Doppler was performed in the patients and in 25 normal subjects.Results:  Tl‐201 uptake defects in the left ventricular myocardium were present in all except one patient (93%). The uptake defects were predominantly located to the anteroseptal and basal posterior segments. Wall motion abnormalities were seen in the same segments, and in addition to this, in the septal area. In line with this, the total amplitude and the peak systolic velocity of mitral annular motion at the septal point were significantly decreased in the patients compared with the control group.Conclusions:  Our data show that left ventricular involvement is common in ARVC. Tl‐201 SPECT and echocardiographic abnormalities were seen not only in patients with long‐lasting symptoms but also in asymptomatic patients and in those with short duration of symptoms.
Comparison between maximal early diastolic velocity in long‐axis direction obtained by M‐mode echocardiography and by tissue Doppler in the assessment of right ventricular diastolic function
Authors: Emilsson K. , Loiske K. , Öhlin B. 
Published: May 2005

SummaryRecently the maximal early diastolic velocity in long‐axis direction of the right ventricle (RV) obtained by tissue Doppler imaging (MDV TDI) has been introduced in the assessment of RV diastolic function (RVDF). There are reasons to think that also the maximal early diastolic velocity in long‐axis direction of the RV obtained using M‐mode echocardiography (MDV TAM) could be used to assess RVDF. Therefore, 29 patients were examined with echocardiography and MDV TAM and MDV TDI were measured and compared. A good correlation (r = 0·76, P<0·001) was found between MDV TAM and MDV TDI indicating that MDV TAM might be used in the assessment of RVDF. However, the velocities obtained by MDV TDI (126·7 ± 38·9 mm s−1) were significantly (P<0·001) higher than the velocities obtained by MDV TAM (78·3 ± 27·8 mm s−1) and the agreement between MDV TAM and MDV TDI was rather poor probably mainly due to differences in the measuring technique. This means that reference values cannot be used interchangeably between MDV TAM and MDV TDI. If MDV TAM is going to be used in the assessment of RVDF new reference values have to be produced if today's technique and recommendations to measure MDV TAM and MDV TDI are used. However, as most new echocardiographs are equipped with PW‐TDI technology it seems preferable to use this technique and compare obtained values with already established reference values.
APN‐Physician Collaboration in Caring for Women With High‐Risk Pregnancies
Authors: Brooten Dorothy , Youngblut JoAnne , Blais Kathleen , Donahue Deborah , Cruz Ivette , Lightbourne Michelle 
Published: May 2005

Purpose

: To examine: (a) frequency and focus of APN‐physician collaborations in a clinical trial in which half of physician prenatal care for women with high‐risk pregnancies was substituted with APN prenatal care delivered in women's homes; and (b) characteristics of women requiring greater numbers of collaborations.
Design and Methods

: Descriptive study with secondary analysis of data from 83 of the original trial's 85 intervention participants followed by APNs prenatally through 8 weeks postpartum. APN practices, recorded in logs, included APN interactions with the women and the physician, and type of APN contact (e.g., home visit, telephone call). Each APN‐physician collaboration was coded for type, timing, and focus.
Findings

: Total number of APN‐physician collaboration contacts was 351, with a mean of 4.5 and a range of 1 to 16 per woman. Focus of collaborations was: status updates (59%), new physical findings (21%), change in treatment (8%), patient concerns (7%) and medication adjustment (5%). No significant differences in numbers of collaborations were found according to age, primary diagnosis, marital status, type of health insurance, race, or income. Women with high school education received more collaborations than did those not completing high school or those with some postsecondary education. Prenatally, women with a first pregnancy required more collaborations than did multipara participants.
Conclusions

: Most APN‐physician collaborative contacts were focused on monitoring women's physical and emotional status and discussing new physical findings. These collaborations were important in the original trial's successful pregnancy and infant outcomes and savings in health care dollars.
A Model of Consequences of Need‐Driven, Dementia‐Compromised Behavior
Authors: Kovach Christine R. , Noonan Patricia E. , Schlidt Andrea Matovina , Wells Thelma 
Published: May 2005

Purpose

: To extend the original need‐driven, dementia‐compromised behavior (NDB) model by explaining the consequences of behavioral symptoms for the person with dementia.
Organizing construct and methods

: Literature is reviewed and the consequences of expressing needs through need‐driven, dementia‐compromised behaviors are posited. The consequences of need‐driven, dementia‐compromised behavior (C‐NDB) theory is proposed as a framework to improve understanding of the person with dementia and the consequences of behavioral symptoms and unmet needs.
Findings

: Instead of normative verbal communication, people with significant dementia commonly communicate need via non‐normative behaviors, making it difficult for caregivers to know that the person has a need and the extent of such need. Not meeting needs of people with dementia affects the person with dementia, care factors, and contextual factors. Cascading effects occur in which not meeting the original need results in new needs and behavioral symptoms.
Conclusions

: This framework indicates the consequences of expressing need behaviorally rather than verbally and shows that caregiver actions might moderate the events that lead to many needs being unresolved. Suggestions are made regarding future research questions deduced from the model.
Processes of Mental Health Service Use by Adolescents with Depression
Authors: Draucker Claire Burke 
Published: May 2005

Purpose

: To begin development of a substantive theory of the processes of mental health service use by adolescents who are depressed and by their families.
Design

: Grounded theory.
Methods

: Open‐ended interviews were conducted with 52 young adults who were depressed as adolescents, four of their parents, and eight professionals who work with adolescents who are depressed. The constant comparison method was used to analyze the data.
Findings

: Adolescents who are depressed and their families perceived several “treatment pitfalls” associated with formal mental health services: (a) “They'll (mental health clinicians) think I'm crazy,” (b) “They'll tell my business,” and (c) “They won't have a clue.” The adolescents and their families interacted with the mental health care providers by engaging in the psychosocial process of “venturing through the system,” that is, proceeding despite possible dangers and risks by steering clear, holding back, and letting it take hold.
Conclusions

: Mental health service use by adolescents with depression involved complex and fluid interactional processes among the depressed adolescents, their parents or caretakers, and mental health care providers. Strategies are needed to avoid creating the pitfalls that concern adolescents and their families.
Education as a Determinant of Career Retention and Job Satisfaction Among Registered Nurses
Authors: Rambur Betty , McIntosh Barbara , Palumbo Mary Val , Reinier Kyndaron 
Published: May 2005

Purpose

: To compare job satisfaction and career retention in two cohorts of RNs, those whose highest degrees were the associate degree (AD) or the bachelor's degree (BS) in nursing.
Design

: Survey.
Methods

: Instruments included a career satisfaction scale and questions based on the ongoing U.S. Health and Retirement Survey. Three‐thousand nurses in the U.S. state of Vermont were surveyed with a resulting response rate of 56.7%. Of these respondents, 878 RNs fit the study criteria.
Findings

: BS RNs started their nursing careers earlier, were employed longer, had held more positions, and in the largest age cohort (age 40–54), were more likely to have been in their current positions at least 10 years. BS RNs scored significantly higher in job satisfaction related to: (a) opportunity for autonomy and growth, (b) job stress and physical demands, and (c) job and organizational security. AD and BS nurses were not significantly different in their satisfaction with supervision; career, continuing education, and promotion opportunities; or pay and benefits.
Conclusions

: These findings indicate support of bachelor's level education for individual and social return on investment, and they show that AD education might have unintended consequences. Implications for the nursing shortage and educational policy are discussed.