bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human health in nature – towards a holistic philosophy of nutrition
Authors: Meyer-Abich Klaus Michael 
Published: October 2005

AbstractObjectiveTo explain how the philosophy of nutrition is part of the philosophy of health. To show that this link allows practical solutions for equity and sustainability.MethodAn analysis of the historical philosophies concerned with nutrition and health. A comparison of the definitions in the history of mind from antiquity to the beginning of the twenty-first century.ConclusionWe are not individually healthy, but we are so in togetherness, even with animals and plants. Comprehensive nutrition science has physical, social and environmental attributes. It follows that nutrition is good for the enhancement of good company with human beings as well as with the connatural world. We recognise that we owe to others what we are and this constitutes the equity of being.
ATID: a web-oriented database for collection of publicly available alternative translational initiation events
Authors: Cai Jun , Zhang Jing , Huang Ying , Li Yanda 
Published: October 2005

Abstract
Summary: Alternative translational initiation is an important cellular mechanism contributing to the diversity of protein products and functions. We develop a database that provides a comprehensive collection of alternative translational initiation events. The purpose of this alternative translational initiation database (ATID) is to facilitate the systematic study of alternative translational initiation of genes. The current version of database contains 300 genes from Homo sapiens, Mus musculus and other species. Each of the genes has two or more isoforms due to alternative translational initiation. Resources in ATID, including gene information, alternative products of genes and domain structures of isoforms, are provided through a user-friendly web interface.
Availability: The ATID database is available for public use at
Contact: caijun99@mails.tsinghua.edu.cn
Supplementary information: Supplementary instructions about this database and further statistical analyses can be found on the web page ()
The influence of missing value imputation on detection of differentially expressed genes from microarray data
Authors: Scheel Ida , Aldrin Magne , Glad Ingrid K. , Sørum Ragnhild , Lyng Heidi , Frigessi Arnoldo 
Published: October 2005

Abstract
Motivation: Missing values are problematic for the analysis of microarray data. Imputation methods have been compared in terms of the similarity between imputed and true values in simulation experiments and not of their influence on the final analysis. The focus has been on missing at random, while entries are missing also not at random.
Results: We investigate the influence of imputation on the detection of differentially expressed genes from cDNA microarray data. We apply ANOVA for microarrays and SAM and look to the differentially expressed genes that are lost because of imputation. We show that this new measure provides useful information that the traditional root mean squared error cannot capture. We also show that the type of missingness matters: imputing 5% missing not at random has the same effect as imputing 10–30% missing at random. We propose a new method for imputation (LinImp), fitting a simple linear model for each channel separately, and compare it with the widely used KNNimpute method. For 10% missing at random, KNNimpute leads to twice as many lost differentially expressed genes as LinImp.
Availability: The R package for LinImp is available at
Contact: idasch@math.uio.no
Supplementary information:
The International Rice Information System. A Platform for Meta-Analysis of Rice Crop Data
Authors: McLaren Christopher Graham , Bruskiewich Richard M. , Portugal Arllet M. , Cosico Alexander B. 
Published: October 2005

Abstract
Ambiguous germplasm identification; difficulty in tracing pedigree information; and lack of integration between genetic resources, characterization, breeding, evaluation, and utilization data are constraints in developing knowledge-intensive crop improvement programs. To address these constraints, the International Crop Information System (www.icis.cgiar.org), a database system for the management and integration of global information on genetic resources and crop improvement for any crop, was developed by genetic resource specialists, crop scientists, and information technicians associated with the Consultative Group for International Agricultural Research and collaborative partners. The International Rice Information System (www.iris.irri.org) is the rice (Oryza species) implementation of the International Crop Information System. New components are now being added to the International Rice Information System to handle the diversity of rice functional genomics data including genomic sequence data, molecular genetic data, expression data, and proteomic information. Users access information in the database through stand-alone programs and Web interfaces, which offer specialized applications and customized views to researchers with different interests.
GrainGenes 2.0. An Improved Resource for the Small-Grains Community
Authors: Carollo Victoria , Matthews David E. , Lazo Gerard R. , Blake Thomas K. , Hummel David D. , Lui Nancy , Hane David L. , Anderson Olin D. 
Published: October 2005

Abstract
GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.
GERMINATE. A Generic Database for Integrating Genotypic and Phenotypic Information for Plant Genetic Resource Collections
Authors: Lee Jennifer M. , Davenport Guy F. , Marshall David , Ellis T.H. Noel , Ambrose Michael J. , Dicks Jo , van Hintum Theo J.L. , Flavell Andrew J. 
Published: October 2005

Abstract
The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.
Combining Experimental and Predicted Datasets for Determination of the Subcellular Location of Proteins in Arabidopsis
Authors: Heazlewood Joshua L. , Tonti-Filippini Julian , Verboom Robert E. , Millar A. Harvey 
Published: October 2005

Abstract
Substantial experimental datasets defining the subcellular location of Arabidopsis (Arabidopsis thaliana) proteins have been reported in the literature in the form of organelle proteomes built from mass spectrometry data (approximately 2,500 proteins). Subcellular location for specific proteins has also been published based on imaging of chimeric fluorescent fusion proteins in intact cells (approximately 900 proteins). Further, the more diverse history of biochemical determination of subcellular location is stored in the entries of the Swiss-Prot database for the products of many Arabidopsis genes (approximately 1,800 proteins). Combined with the range of bioinformatic targeting prediction tools and comparative genomic analysis, these experimental datasets provide a powerful basis for defining the final location of proteins within the wide variety of subcellular structures present inside Arabidopsis cells. We have analyzed these published experimental and prediction data to answer a range of substantial questions facing researchers about the veracity of these approaches to determining protein location and their interrelatedness. We have merged these data to form the subcellular location database for Arabidopsis proteins (SUBA), providing an integrated understanding of protein location, encompassing the plastid, mitochondrion, peroxisome, nucleus, plasma membrane, endoplasmic reticulum, vacuole, Golgi, cytoskeleton structures, and cytosol (www.suba.bcs.uwa.edu.au). This includes data on more than 4,400 nonredundant Arabidopsis protein sequences. We also provide researchers with an online resource that may be used to query protein sets or protein families and determine whether predicted or experimental location data exist; to analyze the nature of contamination between published proteome sets; and/or for building theoretical subcellular proteomes in Arabidopsis using the latest experimental data.
Characterizing the Grape Transcriptome. Analysis of Expressed Sequence Tags from Multiple Vitis Species and Development of a Compendium of Gene Expression during Berry Development
Authors: Goes da Silva Francisco , Iandolino Alberto , Al-Kayal Fadi , Bohlmann Marlene C. , Cushman Mary Ann , Lim Hyunju , Ergul Ali , Figueroa Rubi , Kabuloglu Elif K. , Osborne Craig , Rowe Joan , Tattersall Elizabeth , Leslie Anna , Xu Jane , Baek JongMin , Cramer Grant R. , Cushman John C. , Cook Douglas R. 
Published: October 2005

AbstractWe report the analysis and annotation of 146,075 expressed sequence tags from Vitis species. The majority of these sequences were derived from different cultivars of Vitis vinifera, comprising an estimated 25,746 unique contig and singleton sequences that survey transcription in various tissues and developmental stages and during biotic and abiotic stress. Putatively homologous proteins were identified for over 17,752 of the transcripts, with 1,962 transcripts further subdivided into one or more Gene Ontology categories. A simple structured vocabulary, with modules for plant genotype, plant development, and stress, was developed to describe the relationship between individual expressed sequence tags and cDNA libraries; the resulting vocabulary provides query terms to facilitate data mining within the context of a relational database. As a measure of the extent to which characterized metabolic pathways were encompassed by the data set, we searched for homologs of the enzymes leading from glycolysis, through the oxidative/nonoxidative pentose phosphate pathway, and into the general phenylpropanoid pathway. Homologs were identified for 65 of these 77 enzymes, with 86% of enzymatic steps represented by paralogous genes. Differentially expressed transcripts were identified by means of a stringent believability index cutoff of ≥98.4%. Correlation analysis and two-dimensional hierarchical clustering grouped these transcripts according to similarity of expression. In the broadest analysis, 665 differentially expressed transcripts were identified across 29 cDNA libraries, representing a range of developmental and stress conditions. The groupings revealed expected associations between plant developmental stages and tissue types, with the notable exception of abiotic stress treatments. A more focused analysis of flower and berry development identified 87 differentially expressed transcripts and provides the basis for a compendium that relates gene expression and annotation to previously characterized aspects of berry development and physiology. Comparison with published results for select genes, as well as correlation analysis between independent data sets, suggests that the inferred in silico patterns of expression are likely to be an accurate representation of transcript abundance for the conditions surveyed. Thus, the combined data set reveals the in silico expression patterns for hundreds of genes in V. vinifera, the majority of which have not been previously studied within this species.
Public Health Nursing Practice Change and Recommendations for Improvement
Authors: Zahner Susan J. , Gredig Quynh‐Nga B. 
Published: October 2005

Abstract
Objectives:
This paper reports the characteristics of recent public health nursing (PHN) practice change experienced by staff‐level public health nurses. Recommendations for improving PHN practice offered by study participants are reported and discussed. Design: A cross‐sectional written survey was used to collect data from 424 public health nurses in 76 local health departments (LHDs) in Wisconsin (68% response rate) in 2003. Characteristics of practice change were identified using a 15‐item‐scaled response set. Recommendations on improving practice were made through responses to an open‐ended survey question. Content analysis was conducted to identify major themes among the responses. Results: PHN practice has become more population focused. Major themes emerging from the recommendations for practice improvement included increasing system and organizational resources, expanding visibility of public health, and strengthening collaboration. Conclusions: Implications for practice include the need for continuing education in concepts and skills required for population‐focused PHN practice, advocacy for more public health resources, and collaboration with academic partners for education and research.
Improving Public Health Nursing Education: Recommendations of Local Public Health Nurses
Authors: Zahner Susan J. , Gredig Quynh‐Nga B. 
Published: October 2005

Abstract
Objectives:
This paper reports recommendations for improving public health nursing (PHN) undergraduate, graduate, and continuing education (CE) made by staff‐level public health nurses working in local health departments (LHDs). Implications for academia and practice are discussed. Design: A cross‐sectional written survey was used to collect data from 424 public health nurses in 76 LHDs in Wisconsin (68% response rate) in 2003. Recommendations for improving undergraduate, graduate, and CE were made through responses to open‐ended survey questions. Content analysis was conducted to identify major themes among responses. Results: Major themes emerging from the recommendations for undergraduate education included the need for more clinical public health experiences and population‐focused practice content. Graduate education improvement recommendations included addressing access barriers and increasing organizational incentives. Improved access and more public health content were the major recommendations for improving CE. Conclusions: Implications for academia focus on increasing opportunities for students to experience population‐focused PHN and to learn organizational and collaborative practice skills, supporting PHN preceptors and building evidence for PHN intervention through research. Implications for practice include the need to expand opportunities for students with LHDs and to collaborate with academic partners for education and research.
Arnold Heller and the lymph pump
Authors: Aukland K. 
Published: October 2005

AbstractThis article reviews studies on lymph propulsion in the lymph vessels by active contraction of the vessels, first described by Arnold Heller in 1869 in German language, and here translated into English. His observations were first confirmed by Beatrice Carrier (1926) and Howard Flory et al. (1927), and several groups were active up to World war II. Few publications appeared in the period 1940‐‐1960, followed by increasing activity and development of new experimental techniques for use both in various experimental animals and in humans. Recently it has been shown that passive lymph flow may add to active propulsion. Both mechanisms depend on lymph formation, i.e. the uptake of interstitial fluid by the initial lymph vessels which is still not well understood.
Left ventricular pressure–volume relationships during normal growth and development in the adult rat – studies in 8‐ and 50‐week‐old male Wistar rats
Authors: Bal M. P. , de Vries W. B. , van der Leij F. R. , van Oosterhout M. F. M. , Baan J. , van der Wall E. E. , van Bel F. , Steendijk P. 
Published: October 2005

AbstractAims:  Left ventricular (LV) pressure–volume relations provide relatively load‐independent indexes of systolic and diastolic LV function, but few data are available on pressure–volume relations during growth and development in the normal adult heart. Furthermore, to quantify intrinsic ventricular function the indexes should be normalized for heart weight. However, in many studies the indexes are reported in absolute terms, or body weight‐correction is used as a surrogate for heart weight‐correction.Methods:  We determined pressure–volume relations in young (8‐week‐old, n = 13) and middle‐aged (50‐week‐old, n = 19) male Wistar rats in relation to their heart and body weights. The animals were anaesthetized and a 2F pressure‐conductance catheter was introduced into the LV to measure pressure–volume relations.Results:  Heart and body weights were significantly higher in the 50‐week‐old rats, whereas the heart‐to‐body weight ratio was significantly lower (2.74 ± 0.32 vs. 4.41 ± 0.37 mg g−1, P < 0.001). Intrinsic systolic function, quantified by the slopes of the end‐systolic pressure–volume relation (EES), the dP/dtMAX vs. end‐diastolic volume relation (S‐dP), and the preload recruitable stroke work relation (PRSW), normalized for heart weight, was slightly decreased in the 50‐week‐old rats (S‐dP: −6%, P < 0.004; PRSW: −3%, P < 0.06). Heart weight‐corrected diastolic indexes were not significant different. The absolute indexes qualitatively showed the same results, but body‐weight corrected pressure–volume indexes showed improved systolic function and significantly depressed diastolic function.Conclusions:  Intrinsic systolic function slightly decreases from the juvenile to the middle‐aged period in normal male Wistar rats. Furthermore, correction of pressure–volume indexes for body weight is not an adequate surrogate for heart weight‐correction in these animals.
Respiratory muscle performance with stretch‐shortening cycle manoeuvres: maximal inspiratory pressure–flow curves
Authors: Tzelepis G. E. , Zakynthinos S. , Mandros C. , Tzelepis E. , Roussos C. 
Published: October 2005

AbstractAim:  To test the hypothesis that the maximal inspiratory muscle (IM) performance, as assessed by the maximal IM pressure–flow relationship, is enhanced with the stretch‐shortening cycle (SSC).Methods:  Maximal inspiratory flow–pressure curves were measured in 12 healthy volunteers (35 ± 6 years) during maximal single efforts through a range of graded resistors (4‐, 6‐, and 8‐mm diameter orifices), against an occluded airway, and with a minimal load (wide‐open resistor). Maximal inspiratory efforts were initiated at a volume near residual lung volume (RV). The subjects exhaled to RV using slow (S) or fast (F) manoeuvres. With the S manoeuvre, they exhaled slowly to RV and held the breath at RV for about 4 s prior to maximal inspiration. With the F manoeuvre, they exhaled rapidly to RV and immediately inhaled maximally without a post‐expiratory hold; a strategy designed to enhance inspiratory pressure via the SSC.Results:  The maximal inspiratory pressure–flow relationship was linear with the S and F manoeuvres (r2 = 0.88 for S and r2 = 0.88 for F manoeuvre, P < 0.0005 in all subjects). With the F manoeuvre, the pressure–flow relationship shifted to the right in a parallel fashion and the calculated maximal power increased by approximately 10% (P < 0.05) over that calculated with the S manoeuvre.Conclusion:  The maximal inspiratory pressure–flow capacity can be enhanced with SSC manoeuvres in a manner analogous to increases in the force–velocity relationship with SSC reported for skeletal muscles.
Force–frequency relation in frog‐ventricle is dependent on the direction of sodium/calcium exchange in diastole
Authors: Subramani S. , Balakrishnan S. , Jyoti T. , Sathishkumar S. , Mohammed A. A. , Arasan S. , Vijayanand C. 
Published: October 2005

AbstractAim:  Force of contraction increases with stimulus‐frequency in mammalian and amphibian hearts under control conditions. Here, we have analysed the mechanism of the force–frequency relation (FFR) in frog‐ventricle.Methods:  Circular strips of frog‐ventricle were subjected to field‐stimulation with frequencies in the range 0.03–0.2 Hz and force recorded on a chart‐recorder. In another protocol, varying rest‐periods were imposed while the preparation beat steadily at 0.2 Hz and the effect of rest on post‐rest beat amplitude was noted.Results:  Under control conditions, a positive FFR and a rest‐induced decay of contraction amplitude (RID) were seen in the frequency range 0.03–0.2 Hz. With cadmium, nifedipine, nickel (40 μmol L−1), ryanodine and adrenaline (all drugs at 10 μmol L−1 concentration, except nickel), the positive FFR and RID seen under control conditions persisted. When the bathing solution contained ouabain (10 μmol L−1) or low external sodium (40 mmol L−1), or high external calcium (5 mmol L−1), the FFR turned negative in the frequency range stated above and there were rest‐induced potentiations (RIP).Conclusion:  When the conditions favour a net leak of calcium in diastole from intracellular stores via the calcium‐extrusive mode of sodium–calcium exchanger (NCX), FFR is positive. An increase in frequency lessens the diastolic interval and therefore the diastolic calcium leak, thereby augmenting force. On the other hand, interventions which favour the calcium‐acquisitive mode of NCX during diastole, changed the pattern of RID to RIP and converted FFR from positive to negative. With net diastolic calcium uptake, there is better store‐filling and therefore higher force at lower frequencies.