bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capturing biological information with class–responsibility–collaboration cards
Authors: Shegogue Daniel , Zheng W. Jim 
Published: September 2004

Abstract
Summary: Class–responsibility–collaboration (CRC) cards have been used extensively in the software industry for defining complex object-oriented software requirements. We have adapted this tool to capture information about biological components, collaborators and responsibilities within these collaborations, which is not captured by current annotation tools. CRC cards should provide a common ground that will facilitate communication between biologist and computer scientists.
Availability: A CRC card template, XML representation and XML schema are freely available at http://people.musc.edu/~zhengw/CRCCard/CRC_Card_Index.html
Contact: zhengw@musc.edu
Supplementary information: Supplemental Figures 1–4.
iPfam: visualization of protein–protein interactions in PDB at domain and amino acid resolutions
Authors: Finn Robert D. , Marshall Mhairi , Bateman Alex 
Published: September 2004

Abstract
Summary: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have implemented a web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. This detailed knowledge relies on the fact that there are a large number of multidomain proteins and protein complexes being deposited in the structure databases. The resource called iPfam is hosted within the Pfam UK website. Most resources focus on the interactions between proteins; iPfam includes these as well as interactions between domains in a single protein.
Availability: iPfam is available on the Web for browsing at http://www.sanger.ac.uk/Software/Pfam/iPfam/; the source-data for iPfam is freely available in relational tables via the ftp site ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/
Contact: rdf@sanger.ac.uk
Production of polyclonal antiserum against recombinant VP28 protein and its application for the detection of white spot syndrome virus in crustaceans
Authors: Yoganandhan K , Syed Musthaq S , Narayanan R B , Sahul Hameed A S 
Published: September 2004

AbstractThe VP28 gene of white spot syndrome virus (WSSV) was cloned into pRSET B expression vector. The VP28 protein was expressed as a protein with a 6‐histidine taq in Escherichia coli GJ1158 with NaCl induction. Antiserum was raised against this recombinant‐VP28 protein in rabbits and it recognized VP28 protein in naturally and experimentally WSSV‐infected shrimp, marine crabs, freshwater prawns and freshwater crabs. The antiserum did not recognize any of the other known WSSV structural proteins. Various organs such as eyestalks, head muscle, gill tissue, heart tissue, haemolymph, tail tissue and appendages were found to be good materials for detection of WSSV using the antiserum and detection of WSSV was successful in experimentally infected Penaeus monodon and P. indicus at 12 and 24 h post‐infection (p.i.), respectively. The antiserum was capable of detecting WSSV in 5 ng of total haemolymph protein from WSSV‐infected shrimp.
Skeletal myopathy in juvenile barramundi, Lates calcarifer (Bloch), cultured in potassium‐deficient saline groundwater
Authors: Partridge G J , Creeper J 
Published: September 2004

AbstractSaline groundwater is being pumped from a number of locations in rural Western Australia to prevent secondary salinity impacting farmland, rural infrastructure and areas with high conservation value. Aquaculture may offset the costs of groundwater pumping, and the suitability of groundwater for finfish aquaculture is being assessed through bioassays. There are marked spatial variations in the ionic composition of saline ground water in Western Australia and this paper describes two bioassays investigating a saline, potassium‐deficient water source that resulted in mortalities in juvenile barramundi, Lates calcarifer (Bloch). Histopathological examination revealed severe degeneration and necrosis of skeletal muscles, marked hyperplasia of branchial chloride cells and renal tubular necrosis. Clinical chemistry findings included hypernatraemia and hyperchloridaemia of the blood plasma and lowered muscle potassium levels. It is concluded that the principal cause of death was skeletal myopathy induced by low water potassium levels.
Histological alterations in the liver of sea bream, Sparus aurata L., caused by short‐ or long‐term feeding with vegetable oils. Recovery of normal morphology after feeding fish oil as the sole lipid source
Authors: Caballero M J , Izquierdo M S , Kjørsvik E , Fernández A J , Rosenlund G 
Published: September 2004

AbstractThis study evaluated the effects of fish oil (FO) replacement by vegetable oils [soybean oil (SO), rapeseed oil (RO), linseed oil (LO)] and subsequent feeding with FO on the liver morphology of sea bream. A short‐term trial (3 months) and long‐term trial (6 months) were carried out feeding sea bream with the following experimental diets: FO100%; SO60% + FO40%; RO60% +FO40%; LO60% + FO40%; SO + RO +LO60% + FO40%. Finally, all groups from the long‐term trial were fed with FO100% for 95 days (washout period). Liver samples were taken for histological and biochemical studies. In both the short‐ and long‐term trials, livers of sea bream fed LO60% and SO + RO + LO60% showed a similar hepatic morphology to that observed in fish fed FO100%. In contrast, sea bream fed SO60% showed an intense steatosis, with foci of swollen hepatocytes containing numerous lipid vacuoles. After the washout period, a considerable reduction of the cytoplasmic vacuolation and the lipid vacuole accumulation were observed in the livers of fish fed the different experimental diets. The results of this study suggested that the type of non‐essential fatty acid, characteristic of vegetable oils, induces the appearance of steatosis in the following order: linoleic acid > linolenic acid > oleic acid. However, the liver alterations found during the experimental periods with vegetable oils are reversible when the fish are re‐fed with a balanced diet (FO100%), indicating the non‐pathological character of these histological changes.
Maternal – neonatal folate and vitamin B12 serum concentrations in Greeks and in Albanian immigrants
Authors: Schulpis K. , Spiropoulos A. , Gavrili S. , Karikas G. , Grigori C. , Vlachos G. , Papassotiriou I. 
Published: September 2004

AbstractBackground  Low folate and vitamin B12 concentrations during pregnancy are implicated with neural tube defects (NTD) and neurological manifestations in the neonates.Aim  To compare serum concentrations of folate and vitamin B12 in 1025 Greek mothers, 908 immigrant Albanian mothers at delivery and in the cord blood of their neonates.Methods  A 30 days food diary was kept from each mother. Folate and vitamin B12 sera concentrations were measured with Bayer ADVIA Centaur System.Results  Energy, carbohydrates and total fat intake were significantly higher in Albanian mothers when compared with those of Greek origin. On the contrary, total protein, and especially animal protein intake were higher in the Greek mothers. Folate intake was similar between the two ethnic groups whereas vitamin B12 intake in Albanians was evaluated lower (1.8 ± 0.13 μg day−1) when compared with that of Greeks (2.8 ± 0.12 μg day−1; P < 0.001). Folate serum concentrations in mothers and newborns were similar (17.7 ± 9.1 and 26.5 ± 15.2 nm versus 18.1 ± 8.6 and 24.6 ± 14.7 nm, respectively P > 0.05) in the two ethnic groups. In contrast, vitamin B12 serum concentration was significantly lower (135.0 ± 19.6 pm) in the Albanian mothers compared with that of Greeks (164.5 ± 17.7 pm, P < 0.0001). Consequently, the vitamin concentrations was found lower in the newborns of Albanian origin (133.6 ± 11.8 pm) compared with that of Greek neonates (213.3 ± 11.4 pm, P < 0.0001).Conclusions  (a) Folate serum concentrations in Greek and Albanian mothers and in their neonates were similar, (b) vitamin B12 serum concentrations, evaluated for first time in these ethnic groups, were significantly low in Albanians, both in mothers and newborns, (c) the low protein and especially the reduced animal protein intake from the Albanian mothers, possibly due to their low socio‐economic status, may be responsible for their decreased vitamin B12 serum concentrations and (d) vitamin B12 supplementation along with an increase of animal protein intake might improve the vitamin serum status in the Albanians.
Audit of successful weight maintenance in adult and paediatric survivors of thermal injury at a UK regional burn centre
Authors: Windle E. M. 
Published: September 2004

AbstractBackground  Thermal injury is associated with significant weight loss, particularly of lean body mass. Weight loss increases the risk of morbidity and increased length of stay (LOS). Appropriate nutrition support can improve these outcomes. The aim of this audit was to evaluate the success of nutrition intervention in minimizing weight loss in adults and children with thermal injury.Method  Patients referred for nutrition support were monitored for weight change during their inpatient care episode. Sixty cases met the study criteria. Admission and discharge weight profiles were identified. The degree of weight loss was calculated. Comparison was made to a recognized standard of acceptable weight loss.Results  On admission five (13.2%) adults were found to be clinically underweight. All children were within the acceptable weight percentile range. Adults demonstrated higher (mean ± SD) percentage weight loss (8.1 ± 6.0%) than children (4.7 ± 4.5%). About 76.7% of all cases met the standard used. More children (95.5%) met the standard than adults (65.8%).Conclusions  Most subjects maintained weight within an acceptable limit during the inpatient episode. Children appeared particularly successful at weight maintenance. Reasons are multifactorial and warrant further investigation.
Validation of energy intake by dietary recall against different methods to assess energy expenditure
Authors: Lof M. , Forsum E. 
Published: September 2004

AbstractObjectives  To compare the validity of dietary recalls and physical activity recalls and investigate some factors influencing this validity. To provide an example showing how procedures based on recalls of physical activity can assess the validity of dietary recalls and identify subjects constantly underreporting their energy intake (EI).Design and subjects  Thirty‐seven women were studied using three 24‐h dietary recalls, two kinds of physical activity recalls, indirect calorimetry and the doubly labelled water method.Results  The EI obtained using dietary recalls were biased with respect to body mass index (BMI) and attitudes towards body weight and dieting, whereas results obtained using a physical activity recall were not. Eighteen women produced underreports (UR), i.e. their average EI was below 76% of total energy expenditure (TEE), whereas 24 women reported an EI that was lower than TEE on all three recall days, i.e. constantly underreporting subjects. A physical activity recall identified 13 URs and 20 of the constantly underreporting subjects.Conclusions  In contrast to estimates of EI, TEE assessed using physical activity recalls was not biased with respect to BMI or attitudes towards body weight and dieting. Recalls of physical activity represent potentially useful procedures for identifying URs and constantly underreporting subjects but are not accurate enough for individuals.
Temperature‐Induced Changes in Fluorescence Properties as a Probe of Porphyrin Microenvironment in Lipid Membranes
Authors: Ricchelli Fernanda , Gobbo Silvano , Jori Giulio , Moreno Giuliana , Salet Christian 
Published: September 2004

Temperature‐induced fluorescence changes were studied for hematoporphyrin and protoporphyrin, incorporated into liposomes of dipalmitoylphosphoglycerocholine (Pam2GroPCho) or dimiristoylphosphoglycerocholine (Myr2GroPCho). In some cases, cholesterol or cardiolipin were added to the vesicles for better mimicking the lipid composition of biological membranes. The experimental conditions were appropriately chosen in order to reproduce different possible configurations of the porphyrin molecule in lipid membranes: namely, at the polar water/headgroups, headgroups/lipid and lipid/lipid interfaces.A peculiar feature observed in some of the above liposomal systems was the appearence of discontinuities in the Arrhenius plots of the fluorescence quantum yields, with relevant changes of the values of activation energies. These discontinuities were due to an increase of the fluorescence signal in a temperature range corresponding to the transition of the different lipids from the gel‐to‐liquid crystal state. The observed phenomena are consistent with the formation of non‐covalent linear dimers or linear higher aggregates of the porphyrin molecules. The intermolecular contacts required for the formation of these species are favored by at least three situations: disruption of the ordered lipid structure during the gel‐to‐liquid crystal phase transition; competition of other polar groups (e.g., the ‐OH group of cholesterol) with the porphyrin carboxylate groups for the polar phospholipid headgroups; and steric constraints due to overcrowding of porphyrin molecules in a restricted space.
Prevention of Cholesteryl Ester Accumulation in P388D1 Macrophage‐Like Cells by Increased Cellular Vitamin E Depends on Species of Extracellular Cholesterol
Authors: Asmis Reto , Llorente Vicenta C. , Gey K. Fred 
Published: September 2004

Since the cellular role of the antioxidative vitamins in the formation of foam cells has not yet been studied in detail, we investigated the effect of α‐tocopherol and ascorbic acid loading of P388D1 macrophage‐like cells on their cholesterol and cholesteryl ester levels and their response to the exposure to different lipoproteins. α‐Tocopherol loading, but not ascorbic acid loading, of P388D1 cells strongly reduced their cellular cholesteryl ester/cholesterol ratio (the crucial indicator of foam cell formation) when fetal calf serum was the only extracellular source of cholesterol. Balance studies suggest that this effect of α‐Tocopherol was mainly due to a reduced uptake of fetal‐calf‐serum‐derived cholesterol. α‐Tocopherol loading, however, did not reduce the cholesteryl ester/cholesterol ratio when human unmodified low‐density lipoprotein (LDL) was added to culture medium containing fetal calf serum. Thus, the uptake of fetal‐calf‐serum‐derived cholesterol was competetively reduced by human LDL, the uptake of which remained unaffected by α‐tocopherol. Similarly, α‐tocopherol loading did not prevent cholesteryl ester formation induced by human LDL either oxidized with Cu2+, ultraviolet light or HOCl, or modified by acetylation, aggregation or by malondialdehyde treatment. The present experimental conditions lacked any pro‐oxidative burden, since (a) ascorbic acid, either alone or combined with α‐tocopherol, did not affect cellular cholesteryl ester levels, (b) foam cell formation was not a linear function of the degree of oxidative LDL modification, and (c) α‐tocopherol lacked specific effects on oxidatively modified LDL. Thus, the reduction of cellular cholesteryl esters by α‐tocopherol in the absence of human unmodified LDL was hardly due to common antioxidative properties of vitamin E.In conclusion, the present observation that a desirable α‐tocopherol effect on the cholesteryl ester balance in mouse‐tumor‐derived P388D1 cells strongly depended on the species of extracellular cholesterol carrier, cautions against premature generalizations of conventional non‐human cell culture data.
Dimeric 3‐Phosphoglycerate Kinases from Hyperthermophilic Archaea
Authors: Hess Daniel , Krüger Kerstin , Knappik Achim , Palm Peter , Hensel Reinhard 
Published: September 2004

The gene coding for the 3‐phosphoglycerate kinase (EC 2.7.2.3) of Pyrococcus woesei was cloned and sequenced. The gene sequence comprises 1230 bp coding for a polypeptide with the theoretical Mr of 46195. The deduced protein sequence exhibits a high similarity (46.1% and 46.6% identity) to the other known archaeal 3‐phosphoglycerate kinases of Methanobacterium bryantii and Methanothermus fervidus [Fabry, S., Heppner, P., Dietmaier, W. & Hensel, R. (1990) Gene 91, 19–25]. By comparing the 3‐phosphoglycerate kinase sequences of the mesophilic and the two thermophilic Archaea, trends in thermoadaptation were confirmed that could be deduced from comparisons of glyceraldehyde‐3‐phosphate dehydrogenase sequences from the same organisms [Zwickl, P., Fabry, S., Bogedain, C., Haas, A. & Hensel, R. (1990) J. Bacteriol. 172, 4329–4338]. With increasing temperature the average hydrophobicity and the portion of aromatic residues increases, whereas the chain flexibility as well as the content in chemically labile residues (Asn, Cys) decreases.To study the phenotypic properties of the 3‐phosphoglycerate kinases from thermophilic Archaea in more detail, the 3‐phosphoglycerate kinase genes from P. woesei and M. fervidus were expressed in Escherichia coli. Comparisons of kinetic and molecular properties of the enzymes from the original organisms and from E. coli indicate that the proteins expressed in the mesophilic host are folded correctly. Besides their higher thermostability according to their origin from hyperthermophilic organisms, both enzymes differ from their bacterial and eucaryotic homologues mainly in two respects, (a) The 3‐phosphoglycerate kinases from P. woesei and M. fervidus are homomeric dimers in their native state contrary to all other known 3‐phosphoglycerate kinases, which are monomers including the enzyme from the mesophilic Archaeum M. bryantii. (b) Monovalent cations are essential for the activity of both archaeal enzymes with K+ being significantly more efficient than Na+. For the P. woesei enzyme, non‐cooperative K+ binding with an apparent Kd (K+) of 88 mM could be determined by kinetic analysis, whereas for the M. fervidus 3‐phosphoglycerate kinase the K+ binding is rather complex: from the fitting of the saturation data, non‐cooperative binding sites with low selectivity for K+ and Na+ (apparent Kd= 270 mM) and at least three cooperative and highly specific K+ binding sites/subunit are deduced.At the optimum growth temperature of P. woesei (100°C) and M. fervidus (83°C), the 3‐phosphoglycerate kinases show half‐lives of inactivation of only 28 min and 44 min, respectively. Potassium salts of polyvalent anions stabilize both 3‐phosphoglycerate kinases, like other enzymes from these organisms. In the case of M. fervidus 3‐phosphoglycerate kinase, the dominant low‐molecular‐mass compound cyclic d‐glycerate 2,3‐bisphosphate found in vivo [Hensel, R. & König, H. (1988) FEMS Microbiol. Lett. 19, 325–333] is the most effective.
Mutations at Positions 11 and 60 of Insulin‐Like Growth Factor 1 Reveal Differences between its Interactions with the Type I Insulin‐Like‐Growth‐Factor Receptor and the Insulin Receptor
Authors: Hodgson Darren R. , May Felicity E. B. , Westley Bruce R. 
Published: September 2004

Insulin‐like growth factor 1 (IGF‐1) and three analogues ([V11I]IGF‐1, [V11T]IGF‐1, and [Y60F]IGF‐1), constructed by site‐directed mutagenesis, were expressed as fusion proteins and secreted into the periplasmic space ofEscherichia coli.Purified IGF were obtained following IgG Sepharose affinity and cation‐exchange chromatographies of the products of hydroxylamine cleavage of fusion proteins. The properties of the mutants were assessed using (a) quantification of affinities for the human insulin receptor overexpressed on NIH 3T3 cells, (b) quantification of affinities for the type I IGF receptor via competition for binding to a monolayer of MDA‐MB‐231 cells, (c) promotion of thein vitromitogenesis of growth‐arrested MCF‐7 cells in the presence of 17‐β‐oestradiol, and (d) a competition assay for binding to IGF‐binding proteins secreted by MCF‐7 cells.The mutants exhibited decreases in affinity for the insulin receptor, relative to IGF‐1, of 2.6‐, 3.8‐and, 8.8‐fold for [Y60F]IGF‐1, [V11I]IGF‐1, and [V11T]IGF‐1, respectively. IGF‐1, [V11I]IGF‐1, and [Y60F]IGF‐1 were of equal potency in the growth assay and in affinity for the type I IGF receptor. [V11 T]IGF‐1 exhibited a three fold loss of potency in the type I IGF receptor‐binding and growth assays. The mutants did not differ significantly from IGF‐1 in their affinities for the IGF‐binding proteins.The full‐activity of [Y60F]IGF‐1 at the type I IGF receptor, in contrast to the weakened receptor affinity of IGF‐1 with a Leu substitution at this position, indicates a requirement for an aromatic ring, rather than a hydroxyl group, in the interaction of IGF‐1 with the type I IGF receptor. The decrease in affinity for the insulin receptor of all the mutants indicates that, as in insulin, the residues Val11 and Tyr60 are important for the interaction of IGF‐1 with the insulin receptor. The unchanged or minor changes in the affinities of the mutants for the type I IGF receptor contrast with the more deleterious effects of the mutations on insulin receptor binding and with the properties of analogues of insulin mutated at equivalent sites: 3‐fold and 5–10‐fold reductions in biological activity for [VB121]insulin and [YA19F]insulin, respectively. Thus, the results obtained using the mutants indicate important differences between the IGF‐1/type I IGF receptor and insulin/insulin receptor interactions.
What is the practical conversion dose when changing from epoetin alfa to darbepoetin outside of clinical trials?
Authors: ROGER SIMON D , COOPER BRUCE 
Published: September 2004

SUMMARY:Background:  The recommended conversion dose for changing from epoetin alfa to darbepoetin alfa is 200 units to 1 µg. However, this may result in the over treatment of uraemic anaemia.Methods:  All in‐centre haemodialysis patients (n = 60) were converted from an existing subcutaneous epoetin alfa regimen to weekly intravenous darbepoetin alfa. The protocol for anaemia management included a target haemoglobin (Hb) concentration of 120–130 g/L and a ferritin of 300–600 µg/L. Patient treatments were converted from subcutaneous epoetin alfa to weekly, intravenous darbepoetin alfa at month 0, at a conversion dose of 200 units epoetin alfa to 1 µg darbepoetin.Results:  Both Hb and ferritin concentrations remained within the target range, but darbepoetin dosages fell from 50.8 to 42.3 µg/week by month 3 (P = 0.02). The initial conversion factor of 210 units/µg rose to 275 units/µg (P = 0.01) at month 4. No difference in conversion dosage could be determined between patients who were epoetin sensitive (<200 units/kg per week) or resistant (>200 units/kg per week, P = NS). Patients were then switched to fortnightly darbepoetin alfa dosing treatments; the existing weekly dose being doubled and Hb levels fell from 125 to 110 g/L (P < 0.0001), despite an increase in the mean dose from 44.9 to 47.5 µg/week (P = 0.02).Conclusion:  The original dosage reduction after the switch from epoetin alfa to weekly intravenous darbepoetin alfa may offset the increased relative cost of the latter. When administered weekly and intravenously, darbepoetin alfa maintains Hb at a more favourable conversion rate than is currently recommended.