bluuebunny/crossref_metadata_2025_split huggingface dataset:
The principles, definition and dimensions of the new nutrition science
Authors: Beauman Christopher , Cannon Geoffrey , Elmadfa Ibrahim , Glasauer Peter , Hoffmann Ingrid , Keller Markus , Krawinkel Michael , Lang Tim , Leitzmann Claus , Lötsch Bernd , Margetts Barrie M , McMichael Anthony J , Meyer-Abich Klaus , Oltersdorf Ulrich , Pettoello-Mantovani Massimo , Sabaté Joan , Shetty Prakash , Sória Marco , Spiekermann Uwe , Tudge Colin , Vorster Hester H , Wahlqvist Mark , Zerilli-Marimò Mariuccia 
Published: October 2005

AbstractObjectiveTo specify the principles, definition and dimensions of the new nutrition science.PurposeTo identify nutrition, with its application in food and nutrition policy, as a science with great width and breadth of vision and scope, in order that it can fully contribute to the preservation, maintenance, development and sustenance of life on Earth.MethodA brief overview shows that current conventional nutrition is defined as a biological science, although its governing and guiding principles are implicit only, and no generally agreed definition is evident. Following are agreements on the principles, definition and dimensions of the new nutrition science, made by the authors as participants at a workshop on this theme held on 5–8 April 2005 at the Schloss Rauischholzhausen, Justus-Liebig University, Giessen, Germany.ResultNutrition science as here specified will retain its current [classical] identity as a biological science, within a broader and integrated conceptual framework, and will also be confirmed as a social and environmental science. As such it will be concerned with personal and population health, and with planetary health – the welfare and future of the whole physical and living world of which humans are a part.
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data
Authors: Boyer Frédéric , Morgat Anne , Labarre Laurent , Pothier Joël , Viari Alain 
Published: October 2005

AbstractMotivation: Modern comparative genomics does not restrict to sequence but involves the comparison of metabolic pathways or protein–protein interactions as well. Central in this approach is the concept of neighbourhood between entities (genes, proteins, chemical compounds). Therefore there is a growing need for new methods aiming at merging the connectivity information from different biological sources in order to infer functional coupling.Results: We present a generic approach to merge the information from two or more graphs representing biological data. The method is based on two concepts. The first one, the correspondence multigraph, precisely defines how correspondence is performed between the primary data-graphs. The second one, the common connected components, defines which property of the multigraph is searched for. Although this problem has already been informally stated in the past few years, we give here a formal and general statement together with an exact algorithm to solve it.Availability: The algorithm presented in this paper has been implemented in C. Source code is freely available for download at:Contact: Alain.Viari@inrialpes.fr
QUASAR—scoring and ranking of sequence–structure alignments
Authors: Birzele Fabian , Gewehr Jan E. , Zimmer Ralf 
Published: October 2005

Abstract
Summary: Sequence–structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence–structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence–structure alignments ranking) provides a unifying framework for scoring sequence–structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against ‘standard-of-truth’ structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.
Availability: The software, examples, the Java documentation and a tutorial are available at
Contact: fabian.birzele@ifi.lmu.de
Comparative Plant Genomics Resources at PlantGDB
Authors: Dong Qunfeng , Lawrence Carolyn J. , Schlueter Shannon D. , Wilkerson Matthew D. , Kurtz Stefan , Lushbough Carol , Brendel Volker 
Published: October 2005

Abstract
PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.
Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress
Authors: Mukherjee Gaurab , Abeygunawardena Niran , Parkinson Helen , Contrino Sergio , Durinck Steffen , Farne Anna , Holloway Ele , Lilja Per , Moreau Yves , Oezcimen Ahmet , Rayner Tim , Sharma Anjan , Brazma Alvis , Sarkans Ugis , Shojatalab Mohammadreza 
Published: October 2005

Abstract
ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data sets represent approximately one-quarter of the experiments in ArrayExpress. The majority are based on Arabidopsis (Arabidopsis thaliana); however, there are other data sets based on Triticum aestivum, Hordeum vulgare, and Populus subsp. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. AtMIAMExpress exports data in MAGE-ML format for upload to any MAGE-ML-compliant application, such as J-Express and ArrayExpress. It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis community. Plant data are queryable both in ArrayExpress and in the Data Warehouse databases, which support queries based on gene-centric and sample-centric annotation. The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk.
Oxidative stress and nitric oxide synthase in skeletal muscles of rats with post‐infarction, compensated chronic heart failure
Authors: Rush J. W. E. , Green H. J. , MacLean D. A. , Code L. M. 
Published: October 2005

AbstractAim:  Involvement of oxidative stress and nitric oxide synthase (NOS) isoforms in skeletal muscle cellular adaptations to chronic heart failure (CHF) is controversial, and possible muscle fibre‐type heterogeneity in the oxidative stress and NOS responses to CHF have not been examined. Consequently, we hypothesized that the changes in determinants of elevated oxidative and nitrosylative stress associated with CHF would occur in skeletal muscle and would be similar in predominantly type I slow twitch muscle (soleus) and type II fast twitch muscle (plantaris) of rats.Methods:  The purpose of this study was to measure NOS isoforms (endothelial, inducible and neuronal NOS) and antioxidant enzymes (SOD‐1, SOD‐2, catalase) by protein immunoblot as well as markers of oxidative stress by biochemical assays in soleus and plantaris muscle sections of the rat hind limb. This was performed for control and post‐infarction, compensated CHF rats.Results:  Twelve weeks after coronary artery ligation‐induced moderate CHF, soleus exhibited decreased SOD‐1, SOD‐2 and eNOS, but increased iNOS and nNOS isoforms assessed by immunoblot. This was associated with elevated lipid and DNA oxidative damage assessed by biochemical assays. In contrast, plantaris muscle exhibited no changes in antioxidant enzymes or NOS isoforms, and had lower lipid and DNA oxidative damage.Conclusion:  These observations suggest a heretofore unreported muscle fibre‐type‐specific response of oxidative stress and NOS isoforms to CHF is of importance in understanding the cellular mechanisms of skeletal muscle dysfunction in CHF.
Saline‐induced natriuresis and renal blood flow in conscious dogs: effects of sodium infusion rate and concentration
Authors: Sandgaard N. C. F. , Andersen J. L. , Holstein‐Rathlou N.‐H. , Bie P. 
Published: October 2005

AbstractAim:  This study focused on static and dynamic changes in total renal blood flow (RBF) during volume expansion and tested whether a change in RBF characteristics is a necessary effector mechanism in saline‐induced natriuresis.Methods:  The aortic flow subtraction technique was used to measure RBF continuously. Identical amounts of NaCl (2.4 mmol kg−1) were given as slow isotonic (Iso, 120 min), slow hypertonic (Hyper, 120 min), and rapid isotonic loads (IsoRapid, 30 min).Results:  During Iso and IsoRapid, arterial blood pressure increased slightly (6–7 mmHg), and during Hyper it remained unchanged. Iso and Hyper increased sodium excretion (4 ± 1 to 57 ± 27 and 10 ± 4 to 79 ± 28 μmol min−1, respectively) and decreased plasma renin activity (by 38% and 29%), angiotensin II (by 56% and 58%) and aldosterone (by 47% and 65%), while RBF remained unchanged. IsoRapid caused a similar increase in sodium excretion (to 72 ± 19 μmol min−1), a similar decrease in renin system activity, but a 15% elevation of RBF (282 ± 22 to 324 ± 35 mL min−1). Selected frequency domain parameters of RBF autoregulation did not change in response to any load.Conclusions:  In response to slow saline loading simulating daily sodium intake, the rate of sodium excretion may increase 10–20‐fold without any change in mean arterial blood pressure or in RBF. Regulatory responses to changes in total body NaCl levels appears, therefore, to be mediated primarily by neurohumoral mechanisms and may occur independent of changes in arterial pressure or RBF.
Effect of carbohydrate ingestion on brain exchange of amino acids during sustained exercise in human subjects
Authors: Blomstrand E. , Møller K. , Secher N. H. , Nybo L. 
Published: October 2005

AbstractAim:  This study investigated the effect of prolonged exercise with and without carbohydrate intake on the brain exchange of amino acids, especially focussing on tryptophan and branched‐chain amino acids (BCAA).Methods:  Five male subjects exercised for 3 h on a cycle ergometer at 200 ± 7 W on two occasions; either supplemented with a 6% carbohydrate solution or with flavoured water (placebo). Catheters were inserted into the right internal jugular vein and the radial artery of the non‐dominant arm. The brain exchange of amino acids during exercise was calculated from the arterial‐jugular venous concentration difference multiplied by plasma flow.Results:  About 106 μmol (22 mg) of tryptophan was taken up by the brain during exercise in the placebo trial, whereas no significant uptake was observed in the carbohydrate trial. In accordance, the arterial concentration of free tryptophan increased from 12 ± 1 to 20 ± 2 μmol L−1 during the placebo trial and was significantly higher compared with the glucose trial (14 ± 1 μmol L−1 at the end of exercise). Also, the arterial concentration of total tryptophan (free and albumin‐bound) increased during the first 30 min of exercise in both trials, but returned to the basal level at 180 min of exercise. In both trials, BCAA were taken up by the brain while glutamine was released.Conclusion:  The present data show that both tryptophan and BCAA are taken up by the brain during prolonged exercise, and we suggest that the cerebral uptake of tryptophan may relate to increased synthesis of serotonin (5‐HT) in the brain.
Effects of innervation state on Hsp25 content and phosphorylation in inactive rat plantaris muscles
Authors: Huey K. A. , Hyatt J.‐P. K. , Zhong H. , Roy R. R. 
Published: October 2005

AbstractAim:  Previous reports suggest a role for neuromuscular activity levels and/or connectivity in modulating Hsp25 expression and phosphorylation (pHsp25) in skeletal muscles. However, pHsp25 has only been studied in denervated muscles and/or muscles exposed to high levels of residual neuromuscular activity. Spinal cord isolation (SI) provides a model in which the muscle is exposed to nearly complete inactivity with maintenance of the nerve–muscle connection. To parcel out the roles of innervation state and activity‐independent neural factors, we compared Hsp25 and pHsp25 in the plantaris of control (Con), SI, and denervated (Den, inactivity without neural connectivity) rats.Methods:  Hsp25 and pHsp25 protein levels (soluble and insoluble fractions) were measured with Western blot analysis after 1, 3, 8, 14, or 28 days of SI or Den. pHsp25 was normalized to non‐pHsp25 at each time point.Results:  Hsp25 was unchanged (days 1, 3 and 14) or increased (days 8 and 28) in the soluble fraction, and decreased (day 1) or increased (days 3, 8 and 14) in the insoluble fraction in Den compared with Con rats. pHsp25 was reduced after 1 and 28 days of Den, but near control levels on days 3, 8, and 14 in the soluble fraction. In the insoluble fraction, pHsp25 levels were lower in Den than Con rats on all days. In both fractions, Hsp25 was lower in SI than Con rats. pHsp25 levels were lower in the soluble fraction and higher in the insoluble fraction in SI than Con rats.Conclusion:  These results suggest that an intact innervation, even in the absence of muscle activation and/or loading, is critical for Hsp25 phosphorylation in the insoluble fraction. However, the time‐dependent decrease in Hsp25 with SI suggests a role for minimal levels of muscle activation and/or loading in maintaining Hsp25 expression during sustained inactivity.
Mitochondrial efficiency in rat skeletal muscle: influence of respiration rate, substrate and muscle type
Authors: Mogensen M. , Sahlin K. 
Published: October 2005

AbstractAim:  To investigate the hypothesis that mitochondrial efficiency (i.e. P/O ratio) is higher in type I than in type II fibres during submaximal rates of respiration.Methods:  Mitochondria were isolated from rat soleus and extensor digitorum longus (EDL) muscles, representing type I and type II fibres, respectively. Mitochondrial efficiency (P/O ratio) was determined with pyruvate (Pyr) or palmitoyl‐l‐carnitine (PC) during submaximal (constant rate of adenosine diphosphate infusion) and maximal (Vmax, state 3) rates of respiration and fitted to monoexponential functions.Results:  There was no difference in Vmax between PC and Pyr in soleus but in EDL Vmax with PC was only 58% of that with Pyr. The activity of 3‐hydroxyacyl‐CoA dehydrogenase was threefold higher in soleus than in EDL. P/O ratio at Vmax was 8–9% lower with PC [2.33 ± 0.02 (soleus) and 2.30 ± 0.02 (EDL)] than with Pyr [2.52 ± 0.03 (soleus) and 2.54 ± 0.03 (EDL)] but not different between the two muscles (P > 0.05). P/O ratio was low at low rates of respiration and increased exponentially when the rate of respiration increased. The asymptotes of the curves were similar to P/O ratio at Vmax. P/O ratio at submaximal respirations was not different between soleus and EDL neither with Pyr nor with PC.Conclusion:  Mitochondrial efficiency, as determined in vitro, was not significantly different in the two fibre types neither at Vmax nor at submaximal rates of respiration. The low Vmax for PC oxidation in EDL may relate to low activity of β‐oxidation.
Spectrum of infection, risk and recommendations for prophylaxis and screening among patients with lymphoproliferative disorders treated with alemtuzumab*
Authors: Thursky Karin A. , Worth Leon J. , Seymour John F. , Miles Prince H. , Slavin Monica A. 
Published: October 2005

SummaryThere is an increasing use of monoclonal antibodies in the treatment of haematological malignancies. Alemtuzumab (Campath‐1H; Ilex Pharmaceuticals, San Antonio, TX, USA) is a monoclonal antibody reactive with the CD52 antigen used as first and second line therapy for two types of lymphoproliferative disorders: chronic lymphocytic leukaemia (CLL), and T‐cell lymphomas [both peripheral (PTCL) and cutaneous (CTCL)]. With alemtuzumab therapy, viral, bacterial and fungal infectious complications are frequent, and may be life threatening. An understanding of the patients at highest risk and duration of risk are important in developing recommendations for empirical management, antimicrobial prophylaxis and targeted surveillance. This review discusses the infection risks associated with these lymphoproliferative disorders and their treatment, and provide detailed recommendations for screening and prophylaxis.
The relationship between maternal depression and child outcomes in a child welfare sample: implications for treatment and policy
Authors: Leschied Alan W. , Chiodo Debbie , Whitehead Paul C. , Hurley Dermot 
Published: October 2005

ABSTRACTMaternal depression is an extremely important parenting variable in relation to child general health. This investigation addressed the issue of maternal depression as it relates to the lives of children seen by child welfare authorities. Maternal depression was investigated in the context of the increasing rate of children coming to the attention of the London and Middlesex Children's Aid Society. A variety of child outcomes including those of particular relevance to child welfare, specifically disorders of attachment and neglect and physical abuse, school‐related variables, conduct disorder and psychological distress, were investigated. The relative contribution of maternal depression along with measures of socioeconomic status and social isolation to childhood risk was examined. Results indicated that the rate of maternal depression doubled during the years 1995–2001. Maternal depression was related to children entering care through wardship. Additional poor child outcomes such as attention deficit disorder, conduct disorder and emotional adjustment were also related to maternal depression. The findings are discussed in terms of treatment and policies that can lower the risk to children through effective intervention with depressed mothers.
Fatherhood and immigration: challenging the deficit theory
Authors: Roer‐Strier Dorit , Strier Roni , Este David , Shimoni Rena , Clark Dawne 
Published: October 2005

ABSTRACTMost immigration studies focus on the negative consequences of immigration for families and for parenting. Immigration is also viewed as a factor that undermines fathers’ capacity to implement their fathering roles. The impact of immigration on fathers has received very little attention. This paper is based on 54 interviews with immigrant fathers to Canada and Israel. Based on qualitative data, the paper investigates immigrant fathers’ perceptions of fatherhood in the midst of cultural change. This paper challenges the widely held notion that immigration itself is a risk factor for fatherhood. It focuses rather on the systemic barriers and obstacles facing immigrant fathers in their new country and the positive opportunities this change presents. Implications for intervention and policies concerning immigrant families are discussed.
Beyond attachment theory and therapy: Towards sensitive and evidence‐based interventions with foster and adoptive families in distress
Authors: Barth Richard P. , Crea Thomas M. , John Karen , Thoburn June , Quinton David 
Published: October 2005

ABSTRACTElements of attachment theory have been embraced by practitioners endeavouring to assist foster and adopted children and their parents. Attachment theory articulates the potential risks of experiencing multiple caregivers; emphasizes the importance of close social relationships to development; and recognizes that substitute parents may not always have close relationships with children who have experienced adversities before joining them. Attachment theory offers concerned parents what they believe to be a scientific explanation about their lack of the close, satisfying parent–child relationship they desire. Yet the scientific base of attachment theory is limited both in terms of its ability to predict future behaviours, and especially with regard to its use as the underpinning theory for therapeutic intervention with children experiencing conduct problems. There is a critical need to review the role of attachment theory in child and family services and to consider its place among other explanations for children's disturbing behaviour. An important step towards pursuing alternative approaches is for researchers and practitioners to understand the reasons the attachment paradigm appeals to so many adoptive and foster parents, given the apparent widespread prevalence of attachment‐based interventions. Such understanding might assist in the development of adoption‐sensitive uses of appropriate evidence‐based treatment approaches.
Research Review: Parents’ service experience – a missing element in research on foster care case outcomes
Authors: Alpert Lily T. 
Published: October 2005

ABSTRACTA large body of child protection literature focuses on termination of parental rights, family reunification, and children's re‐entry into care as outcomes for children in foster care. Studies have investigated child, placement, family, and parent variables as predictors of case outcome. However, one important group of variables remains largely unstudied: factors related to parents’ service experience. Parents’ service experience includes parents’ perceptions of and involvement in the various services in which they must participate in order to recover their children from foster care (e.g. mandated treatment programmes such as substance abuse rehabilitation, parenting skills classes, etc.). The parental perspective on the foster care process is a critical element in the life of a child protection case, and its influence on case outcome must be explored. A brief review of the current literature on case outcome predictors is provided and parents’ service experience is highlighted as an area in need of investigation. Suggestions for the measurement of parents’ service experience are also offered.