bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dopamine: the rewarding years
Authors: Marsden Charles A 
Published: January 2006

Dopamine has moved from being an insignificant intermediary in the formation of noradrenaline in 1957 to its present‐day position as a major neurotransmitter in the brain. This neurotransmitter is involved in the control of movement and Parkinson's disease, the neurobiology and symptoms of schizophrenia and attention deficit hyperactivity disorder. It is also considered an essential element in the brain reward system and in the action of many drugs of abuse. This evolution reflects the ability of several famous names in neuropharmacology, neurology and psychiatry to apply new techniques to ask and answer the right questions. There is now excellent knowledge about the metabolism of dopamine, dopamine receptor systems and the structural organisation of dopamine pathways in the brain. Less is known about the function of the different receptors and how the various dopamine pathways are organised to produce normal behaviour, which exhibits disruption in the disease states mentioned. In particular, we have very limited information as to why and how the dopamine system dies or becomes abnormal in Parkinson's disease or a neurodevelopmental disorder such as schizophrenia. Dopamine neurones account for less than 1% of the total neuronal population of the brain, but have a profound effect on function. The future challenge is to understand how dopamine is involved in the integration of information to produce a relevant response rather than to study dopamine in isolation from other transmission systems. This integrated approach should lead to greater understanding and improved treatment of diseases involving dopamine.British Journal of Pharmacology (2006) 147, S136–S144. doi:10.1038/sj.bjp.0706473
Phosphodiesterase inhibitors
Authors: Boswell‐Smith Victoria , Spina Domenico , Page Clive P 
Published: January 2006

Phosphodiesterases are a diverse family of enzymes that hydrolyse cyclic nucleotides and thus play a key role in regulating intracellular levels of the second messengers cAMP and cGMP, and hence cell function. Theophylline and papaverine have historically been used therapeutically and are known to be weak inhibitors of PDE, but to what extent this contributed toward their clinical efficacy was poorly defined. However, the discovery of 11 isoenzyme families and our increased understanding of their function at the cell and molecular level provides an impetus for the development of isoenzyme selective inhibitors for the treatment of various diseases. This review focuses on the development of PDE3 inhibitors for congestive heart failure, PDE4 inhibitors for inflammatory airways disease and most successfully, PDE5 inhibitors for erectile dysfunctionBritish Journal of Pharmacology (2006) 147, S252–S257. doi:10.1038/sj.bjp.0706495
Influence of iothalamate on renal medullary perfusion and oxygenation in the rat
Authors: Liss P. , Aukland K. , Carlsson P.-O. , Palm F. , Hansell P. 
Published: January 2006

Purpose: To evaluate controversial results regarding the effect of the contrast medium (CM) iothalamate on renal medullary blood flow by applying two different methods simultaneously. Material and Methods: The outer medullary blood flow (OMBF) response was estimated using laser-Doppler flowmetry and hydrogen gas wash-out (microelectrodes) simultaneously. Outer medullary oxygen tension (PO2) was measured using Clark type microelectrodes. Iothalamate was injected i.v. at 1600 mg I/kg body weight for 2 min. Results: CM induced a transient 28% decrease in OMBF as measured with the laser Doppler. The hydrogen gas wash-out rate was reduced by 50%, indicating a reduced perfusion. CM induced a transient 60% reduction in PO2, while renal fluid and electrolyte excretion increased several fold. Conclusion: The CM iothalamate reduces outer medullary perfusion as estimated by two different techniques applied simultaneously. The PO2 in the same region was also reduced. Previous controversies regarding the effect of iothalamate on OMBF can be explained by extreme dosage and injection rates greatly exceeding clinical relevance.
Contrast-medium-induced nephropathy correlated to the ratio between dose in gram iodine and estimated gfr in ml/min
Authors: Nyman U. , Almén T. , Aspelin P. , Hellström M. , Kristiansson M. , Sterner Gunnar 
Published: January 2006

Purpose: To suggest a more precise tool when assessing the risk of contrast-medium-induced nephropathy (CIN), i.e. the ratio between contrast medium (CM) dose expressed in grams of iodine (g-I) and estimated glomerular filtration rate in ml/min (eGFR; based on equations using serum-creatinine (s-Cr), weight, height, age, and/or sex), here named I-dose/GFR ratio. Material and Methods: A Medline search of published CIN investigations reporting mean eGFR and mean dose of low-osmolality CM (LOCM) identified 10 randomized controlled prophylactic and 2 cohort coronary investigations, and 3 randomized and 1 cohort computed tomographic (CT) investigation. From the randomized trials, data were collected only from the placebo or control arms, unless there was no significant difference between the control and test groups. The mean I-dose/GFR ratio of each study was correlated with the mean frequency of CIN-1 (s-Cr rise⩾44.2 µmol/l or ⩾20–25%) and CIN-2 (oliguria or requiring dialysis). A maximum dose according to an I-dose/GFR ratio = 1 in patients with s-Cr ranging from 100 to 300 µmol/l was compared with that of Cigarroa's formula and with a “European consensus” threshold published by the European Society of Urogenital Radiology, both using s-Cr alone to predict renal function. McCullough's formula was used to assess the risk of CIN requiring dialysis at an I-dose/GFR ratio = 1 with LOCM. Results: The coronary investigations revealed a linear correlation with a correlation coefficient between the I-dose/GFR ratio and the frequency of CIN-1 and CIN-2 of 0.91 ( P<0.001) and 0.84 ( P = 0.001), respectively. At a mean I-dose/GFR ratio = 1, the regression line indicated a 10% risk of CIN-1 and a 1% risk of CIN-2. At a mean I-dose/GFR ratio = 3, the risk of CIN-1 and CIN-2 increased to about 50% and 15%, respectively. Pooled weighted data from the CT investigations revealed a 12% risk of CIN-1 at a mean I-dose/GFR ratio = 1.1 and no cases of CIN-2. The maximum CM dose according to an I-dose/GFR ratio = 1 was about 30–50% of that of both Cigarroa's formula and the “European consensus” in elderly low-weight individuals, while it was similar for middle-aged individuals weighing about 90 kg. McCullough's formula suggests that there will be an exponentially increasing risk of CIN requiring dialysis, but at an I-dose/GFR ratio = 1 and using LOCM it will not exceed 1% until GFR decreases below 30 ml/min in diabetics and below 20 ml/min in non-diabetics. Conclusion: Using the I-dose/GFR ratio may be a more expedient way of improving risk assessment of CIN than today's common practice of estimating CM dose from volume alone and renal function from s-Cr alone. Prospective studies based on individual patient data are encouraged to define the risk of CIN at various I-dose/GFR ratios and correlated to type of CM, examination, risk factors, etc.
Angulation, length, and morphology of the styloid process of the temporal bone analyzed by multidetector computed tomography
Authors: Onbas O. , Kantarci M. , Murat Karasen R. , Durur I. , Cinar Basekim C. , Alper F. , Okur A. 
Published: January 2006

Purpose: To investigate the angulation, length, and structural variations of the styloid process (SP) by multidetector computed tomography (MDCT). Material and Methods: MDCT scans were performed in 283 cases (127 M and 156 F, age range 18–77 years). The length of the SP and its angulation on the transverse and sagittal planes were measured. Structural variations of the SP were observed by means of three-dimensional (3D) and multiplanar reconstruction (MPR) images. Results: The length of the bony SP on both sides varied from 0 to 62 mm (mean 26.8±10.0 mm). Angulation ranged between 55° and 90.5° (7 2.7±6.6) in the transversal plane and between 76° and 110° (93.5±6.9) in the sagittal plane. Morphologically, the SP showed a considerable amount of variation. A solitary SP was present in 168 individuals (59.4%). In 9 individuals (3.1%), the SP was duplicated (4 unilateral and 5 bilateral). Sixty-one persons (21.6%) showed an incomplete ossified SP (42 unilateral and 19 bilateral), whereas in 7 individuals (2.5%) a bony SP was absent entirely (7 unilateral). In 38 individuals (13.4%), the stylohyoid ligament was ossified (16 entirely, 22 partial). In all individuals, 3D and MPR images showed the SP in its entire length. Conclusion: MDCT with 3D CT and MPR of SP may show further detailed information related to SP. Not only the length of the SP, but also its 3D orientation, should be in focus in anatomical and clinical studies.
A regularized discriminative model for the prediction of protein–peptide interactions
Authors: Lehrach Wolfgang P. , Husmeier Dirk , Williams Christopher K. I. 
Published: January 2006

Abstract
Motivation: Short well-defined domains known as peptide recognition modules (PRMs) regulate many important protein–protein interactions involved in the formation of macromolecular complexes and biochemical pathways. Since high-throughput experiments like yeast two-hybrid and phage display are expensive and intrinsically noisy, it would be desirable to more specifically target or partially bypass them with complementary in silico approaches. In the present paper, we present a probabilistic discriminative approach to predicting PRM-mediated protein–protein interactions from sequence data. The model is motivated by the discriminative model of Segal and Sharan as an alternative to the generative approach of Reiss and Schwikowski. In our evaluation, we focus on predicting the interaction network. As proposed by Williams, we overcome the problem of susceptibility to over-fitting by adopting a Bayesian a posteriori approach based on a Laplacian prior in parameter space.
Results: The proposed method was tested on two datasets of protein–protein interactions involving 28 SH3 domain proteins in Saccharmomyces cerevisiae, where the datasets were obtained with different experimental techniques. The predictions were evaluated with out-of-sample receiver operator characteristic (ROC) curves. In both cases, Laplacian regularization turned out to be crucial for achieving a reasonable generalization performance. The Laplacian-regularized discriminative model outperformed the generative model of Reiss and Schwikowski in terms of the area under the ROC curve on both datasets. The performance was further improved with a hybrid approach, in which our model was initialized with the motifs obtained with the method of Reiss and Schwikowski.
Availability: Software and supplementary material is available from
Contact: wlehrach@ed.ac.uk
A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model
Authors: Catanzaro Daniele , Pesenti Raffaele , Milinkovitch Michel C. 
Published: January 2006

Abstract
Motivation: The general-time-reversible (GTR) model is one of the most popular models of nucleotide substitution because it constitutes a good trade-off between mathematical tractability and biological reality. However, when it is applied for inferring evolutionary distances and/or instantaneous rate matrices, the GTR model seems more prone to inapplicability than more restrictive time-reversible models. Although it has been previously noted that the causes for intractability are caused by the impossibility of computing the logarithm of a matrix characterised by negative eigenvalues, the issue has not been investigated further.
Results: Here, we formally characterize the mathematical conditions, and discuss their biological interpretation, which lead to the inapplicability of the GTR model. We investigate the relations between, on one hand, the occurrence of negative eigenvalues and, on the other hand, both sequence length and sequence divergence. We then propose a possible re-formulation of previous procedures in terms of a non-linear optimization problem. We analytically investigate the effect of our approach on the estimated evolutionary distances and transition probability matrix. Finally, we provide an analysis on the goodness of the solution we propose. A numerical example is discussed.
Contact: mcmilink@ulb.ac.be
ANDY: a general, fault-tolerant tool for database searching on computer clusters
Authors: Smith Andrew , Chandonia John-Marc , Brenner Steven E. 
Published: January 2006

Abstract
Summary: ANDY (seArch coordination aND analYsis) is a set of Perl programs and modules for distributing large biological database searches, and in general any sequence of commands, across the nodes of a Linux computer cluster. ANDY is compatible with several commonly used distributed resource management (DRM) systems, and it can be easily extended to new DRMs. A distinctive feature of ANDY is the choice of either dedicated or fair-use operation: ANDY is almost as efficient as single-purpose tools that require a dedicated cluster, but it runs on a general-purpose cluster along with any other jobs scheduled by a DRM. Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms.
Availability: ANDY is freely available and can be obtained from
Contact: brenner@compbio.berkeley.edu
Supplementary information: Supplemental data, figures, and a more detailed overview of the software are found at
OPM: Orientations of Proteins in Membranes database
Authors: Lomize Mikhail A. , Lomize Andrei L. , Pogozheva Irina D. , Mosberg Henry I. 
Published: January 2006

Abstract
Summary: The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading.
Availabililty:
Contact: almz@umich.edu
BuchneraBASE: a post-genomic resource for Buchnera sp. APS
Authors: Prickett M. Dennis , Page Matt , Douglas Angela E. , Thomas Gavin H. 
Published: January 2006

Abstract
Summary: BuchneraBASE is a bioinformatic research tool for the genome of the symbiotic bacterium Buchnera sp. APS that includes an improved genome annotation, comparative information about related insect symbiont genomes and a complete mapping of metabolic reactions to an Escherichia coli in silico model. The database is designed to accommodate genome-wide post-genomic datasets that are becoming available for this organism.
Availability: BuchneraBASE is available at
Contact: ght2@york.ac.uk
A multi-step approach to time series analysis and gene expression clustering
Authors: Amato R. , Ciaramella A. , Deniskina N. , Mondo C. Del , di Bernardo D. , Donalek C. , Longo G. , Mangano G. , Miele G. , Raiconi G. , Staiano A. , Tagliaferri R. 
Published: January 2006

AbstractMotivation: The huge growth in gene expression data calls for the implementation of automatic tools for data processing and interpretation.Results: We present a new and comprehensive machine learning data mining framework consisting in a non-linear PCA neural network for feature extraction, and probabilistic principal surfaces combined with an agglomerative approach based on Negentropy aimed at clustering gene microarray data. The method, which provides a user-friendly visualization interface, can work on noisy data with missing points and represents an automatic procedure to get, with no a priori assumptions, the number of clusters present in the data. Cell-cycle dataset and a detailed analysis confirm the biological nature of the most significant clusters.Availability: The software described here is a subpackage part of the ASTRONEURAL package and is available upon request from the corresponding author.Contact: robtag@unisa.itSupplementary information: Supplementary data are available at Bioinformatics online.
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
Authors: Montgomery S. B. , Griffith O. L. , Sleumer M. C. , Bergman C. M. , Bilenky M. , Pleasance E. D. , Prychyna Y. , Zhang X. , Jones S. J. M. 
Published: January 2006

Abstract
Motivation: Our understanding of gene regulation is currently limited by our ability to collectively synthesize and catalogue transcriptional regulatory elements stored in scientific literature. Over the past decade, this task has become increasingly challenging as the accrual of biologically validated regulatory sequences has accelerated. To meet this challenge, novel community-based approaches to regulatory element annotation are required.
Summary: Here, we present the Open Regulatory Annotation (ORegAnno) database as a dynamic collection of literature-curated regulatory regions, transcription factor binding sites and regulatory mutations (polymorphisms and haplotypes). ORegAnno has been designed to manage the submission, indexing and validation of new annotations from users worldwide. Submissions to ORegAnno are immediately cross-referenced to EnsEMBL, dbSNP, Entrez Gene, the NCBI Taxonomy database and PubMed, where appropriate.
Availability: ORegAnno is available directly through MySQL, Web services, and online at . All software is licensed under the Lesser GNU Public License (LGPL).
Contact: sjones@bcgsc.ca
A paired study of prairie carbon stocks, fluxes, and phenology: comparing the world's oldest prairie restoration with an adjacent remnant
Authors: KUCHARIK CHRISTOPHER J. , FAYRAM NATHAN J. , CAHILL KIMBERLY NICHOLAS 
Published: January 2006

AbstractWe measured carbon (C) stocks and fluxes and vegetation phenology in the world's oldest prairie restoration (∼65 years) and an adjacent prairie remnant in southern Wisconsin from 2001–2004 to quantify structural and functional differences. While the species distributions and frequency differed, the number of species measured per 1 m2quadrat were not significantly different (15.8±4.4 and 14.1±2.1 for remnant and planted [order for all reported values in abstract];P=0.29), and the annual average aboveground net primary productivity (271±51 and 330±55 g C m−2) and peak leaf area index (2.9–4.9 m2 m−2) were comparable under similar fire management. Total root biomass was not significantly different in 2002 (1736±1062 and 1690±459 g dry matter m−2) or 2003 (3029±2081 and 2146±898 g m−2), but annual average soil respiration (1229±77 and 1428±24 g C m−2 yr−1) was significantly higher in the restoration (P<0.0001). However, the prairie remnant contained 37% greater soil C (P<0.0001) in the top 25 cm. Soil respiration response to 10 cm soil temperature (Q10) varied with respect to prairie and soil moisture conditions as annualQ10values ranged from 2.5 to 3.6. We calculated a range of net ecosystem production (NEP) values using estimated heterotrophic respiration and three root turnover values. Average NEP varied from −1.4 to 1.9 and −2.3 to 1.3 Mg C ha−1 yr−1for the remnant and planted prairies, respectively. While these two prairies share similar structural components and functional attributes, the large uncertainty in NEP casts doubt as to whether we can verify these prairies as C sources or sinks without direct measures of heterotrophic respiration and root turnover. We argue that quantitative studies of C exchange in prairies, which differ in restoration methodology, management intensity, and fire frequency, are needed to solidify the relationship between prairie structure and potentially desired functions such as C sequestration.
Effect of improved nitrogen management on greenhouse gas emissions from intensive dairy systems in the Netherlands
Authors: SCHILS R. L. M. , VERHAGEN A. , AARTS H. F. M. , KUIKMAN P. J. , ŠEBEK L. B. J. 
Published: January 2006

AbstractDairy systems in Europe contribute to the emissions of the greenhouse gases (GHGs) nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2). In this paper, the effects of improved nitrogen (N) management on GHG emissions from Dutch dairy farms are determined. The GHG emissions are calculated using the panel on climate change (IPCC) methodology for the Netherlands, an updated and refined IPCC methodology, and a full accounting approach.The changes in dairy farming over the last 20 years, and the consequences for N management are described using detailed farm‐level data, collected in 1985, 1997 and 2002. The selected years represent distinct stages in the implementation of N policies. The changes in N management have reduced the GHG emissions. A reduction of the N surplus per kilogram milk with 1 g N reduced the GHG emissions per kilogram milk with approximately 29 g CO2‐equivalents. The reduction of the N surpluses was mainly brought about by reduced fertilizer use and reduced grazing time. The use of updated and refined emission factors resulted in higher CH4emissions and lower N2O emissions. On average, the overall emission was 36% higher with the refined method. Full accounting, including all direct and indirect emissions of CH4, N2O and CO2, increased the emission with 36% compared with the refined IPCC methodology.We conclude that the N surplus at farm level is a useful indicator of GHG emissions.A full accounting system as presented in this study may effectively enable farmers to address the issue of emissions of GHGs in their operational management decisions. Both approaches serve their own specific objectives: full accounting at the farm level to explore mitigation options, and the IPCC methods to report changes in GHG emissions at the national level.
Comparison of measured and EF5‐r‐derived N2O fluxes from a spring‐fed river
Authors: CLOUGH TIM J. , BERTRAM JANET E. , SHERLOCK ROBERT R. , LEONARD ROBERT L. , NOWICKI BARBARA L. 
Published: January 2006

AbstractThere is considerable uncertainty in the estimates of indirect N2O emissions as defined by the intergovernmental panel on climate change's (IPCC) methodology. Direct measurements of N2O yields and fluxes in aquatic river environments are sparse and more data are required to determine the role that rivers play in the global N2O budget.The objectives of this research were to measure the N2O fluxes from a spring‐fed river, relate these fluxes to the dissolved N2O concentrations and NO3‐N loading of the river, and to try and define the indirect emission factor (EF5‐r) for the river.Gas bubble ebullition was observed at the river source with bubbles containing 7.9 μL N2O L−1. River NO3‐N and dissolved N2O concentrations ranged from 2.5 to 5.3 mg L−1 and 0.4 to 1.9 μg N2O‐N L−1, respectively, with N2O saturation reaching 404%. Floating headspace chambers were used to sample N2O fluxes. N2O‐N fluxes were significantly related to dissolved N2O‐N concentrations (r2=30.6) but not to NO3‐N concentrations. The N2O‐N fluxes ranged from 38–501 μg m−2 h−1, averaging 171 μg m−2 h−1 (±SD 85) overall. The measured N2O‐N fluxes equated to an EF5‐r of only 6.6% of that calculated using the IPCC methodology, and this itself was considered to be an overestimate because of the degassing of antecedent dissolved N2O present in the groundwater that fed the river.