bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural characterization of proteins using residue environments
Authors: Mooney Sean D. , Liang Mike Hsin‐Ping , DeConde Rob , Altman Russ B. 
Published: October 2005

AbstractA primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence‐independent method called S‐BLEST (Structure‐Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S‐BLEST encodes the local environment of an amino acid as a vector of structural property values. It has been applied to all amino acids in a nonredundant database of protein structures to generate a searchable structural resource. Given a query amino acid from an experimentally determined or modeled structure, S‐BLEST quickly identifies similar amino acid environments using a K‐nearest neighbor search. In addition, the method gives an estimation of the statistical significance of each result. We validated S‐BLEST on X‐ray crystal structures from the ASTRAL 40 nonredundant dataset. We then applied it to 86 crystallographically determined proteins in the protein data bank (PDB) with unknown function and with no significant sequence neighbors in the PDB. S‐BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The Protein Circular Dichroism Data Bank (PCDDB): A bioinformatics and spectroscopic resource
Authors: Wallace B. A. , Whitmore Lee , Janes Robert W. 
Published: October 2005

AbstractThis article describes the development and creation of the Protein Circular Dichroism Data Bank (PCDDB), a deposition and searchable data bank for validated circular dichroism spectra located at http://pcddb.cryst.bbk.ac.uk/. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Molecular docking of balanol to dynamics snapshots of protein kinase A
Authors: Wong Chung F. , Kua Jeremy , Zhang Yingkai , Straatsma T.P. , McCammon J. Andrew 
Published: October 2005

AbstractEven if the structure of a receptor has been determined experimentally, it may not be a conformation to which a ligand would bind when induced fit effects are significant. Molecular docking using such a receptor structure may thus fail to recognize a ligand to which the receptor can bind with reasonable affinity. Here, we examine one way to alleviate this problem by using an ensemble of receptor conformations generated from a molecular dynamics simulation for molecular docking. Two molecular dynamics simulations were conducted to generate snapshots for protein kinase A: one with the ligand bound, the other without. The ligand, balanol, was then docked to conformations of the receptors presented by these trajectories. The Lamarckian genetic algorithm in Autodock [Goodsell et al. J Mol Recognit 1996;9(1):1–5; Morris et al. J Comput Chem 1998;19(14):1639–1662] was used in the docking. Three ligand models were used: rigid, flexible, and flexible with torsional potentials. When the snapshots were taken from the molecular dynamics simulation of the protein–ligand complex, the correct docking structure could be recovered easily by the docking algorithm in all cases. This was an easier case for challenging the docking algorithm because, by using the structure of the protein in a protein–ligand complex, one essentially assumed that the protein already had a pocket to which the ligand can fit well. However, when the snapshots were taken from the ligand‐free protein simulation, which is more useful for a practical application when the structure of the protein–ligand complex is not known, several clusters of structures were found. Of the 10 docking runs for each snapshot, at least one structure was close to the correctly docked structure when the flexible‐ligand models were used. We found that a useful way to identify the correctly docked structure was to locate the structure that appeared most frequently as the lowest energy structure in the docking experiments to different snapshots. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Binding energy analysis for wild‐type and Y181C mutant HIV‐1 RT/8‐Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method
Authors: Saen‐oon Suwipa , Kuno Mayuso , Hannongbua Supa 
Published: October 2005

AbstractTwo‐layered and three‐layered ONIOM calculations were performed to compare the binding energies of 8‐Cl TIBO inhibitor when bound into the human immunodeficiency virus reverse transcriptase binding pocket and a Y181C variant. Both consisted of 20 residues within a radius of 15 Å. A combination of different methods [MP2/6‐31G(d), B3LYP/6‐31G(d,p), and PM3] were performed to take advantage of ONIOM's layering strategy analysis. The obtained results clearly indicate that the Y181C mutation reduces the binding affinity and stability of the inhibitor by approximately 8–9 kcal/mol as obtained from different combined MO:MO methods. Analyses regarding the energetic components of the interaction and deformation energies for 8‐Cl TIBO inhibitor upon binding were also examined extensively. Additional calculations involving the interaction energies between 8‐Cl TIBO with individual residues surrounding the binding pocket were performed at MP2/6‐31G(d,p) and B3LYP/6‐31G(d,p) levels of theory to gain more insight into the energetic differences of wild‐type and Y181C mutant type at the atomistic level. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Nonlinear excitations in self‐assembled one‐dimensional quantum dot arrays
Authors: Amuda Rajamani , Krishnan Ramya 
Published: October 2005

AbstractSelf‐assembled quantum dot arrays are modeled by one‐dimensional Heisenberg ferromagnetic spin chains. The interdot interaction is responsible for the ferromagnetic ordering. Starting from the Heisenberg Hamiltonian, using Bosonic operators coupled with Glauber's coherent state ansatz, the equation of motion is derived. In the lower order of the expansion parameters the dynamics is found to be governed by the nonlinear Schrödinger equation which admits soliton solution. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetic behavior in Ce1–xTbxMn2Si2 silicides by XRD, DSC and AC susceptibility measurements
Authors: Kervan S. , Kılıç A. , Aksu E. , Gencer A. 
Published: October 2005

AbstractThe structural and magnetic properties the polycrystalline Ce1–xTbxMn2Si2 (0 ≤ x ≤ 1) compounds were studied by means of X‐ray powder diffraction, AC susceptibility and differential scanning calorimetry (DSC). All compounds investigated crystallize in the body‐centred tetragonal ThCr2Si2‐type structure with the space group I4/mmm. Substitution of Tb for Ce leads to a linear decrease of the lattice constants and the unit cell volume. The lattice constants and the unit cell volume obey Vegard's law. At low temperatures, the rare earth sublattice orders and reconfigures the ordering in the Mn sublattice for x ≥ 0.2. The Néel temperature TN(Mn) determined by DSC technique increases linearly with increasing Tb content x. The results are collected in the x–T magnetic phase diagram. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Disruption of LRG1 inhibits mother–daughter separation in Saccharomyces cerevisiae
Authors: Svarovsky Michael J. , Palecek Sean P. 
Published: October 2005

AbstractLRG1, previously characterized as a Rho‐GAP that regulates β‐1,3‐glucan synthesis, was identified using a filtration screen designed to isolate genes that promote cell aggregation in Σ1278b Saccharomyces cerevisiae. Disruption of LRG1 in haploid cells resulted in enhanced invasive growth and a strain‐specific ‘clustered’ phenotype that is a consequence of failed separation of mother and daughter cells. Genetic analysis revealed that clustering required functional ROM2, FKS1 and STE12 but not FLO8 or FLO11. Additionally, this phenotype required sufficient nitrogen. β‐1,3‐Glucan content was elevated in lrg1 haploids and these cells possessed a thicker cell wall and septum than wild‐type strains. Additional glucan at the bud site inhibited separation of lrg1 mutants as the clustered phenotype was repressed by expression of the glucanases ENG1 or EGT2. Copyright © 2005 John Wiley & Sons, Ltd.
Genetic/genomic evidence for a key role of polarized endocytosis in filamentous differentiation of S. cerevisiae
Authors: Wu Xiaofeng , Jiang Yi Wei 
Published: October 2005

AbstractUnicellular S. cerevisiae cells switch from the yeast form to pseudohyphal or filamentous form in response to environmental cues. We report that wild‐type BY diploids (in which yeast ORFs have been systematically deleted) undergo normal HU‐induced filamentous growth and discernable nitrogen starvation‐induced filamentous growth, despite their perceived filamentation‐deficient S288C genetic background. This finding allowed us to perform a genome‐wide survey for non‐essential genes that are required for filamentous growth with the homozygous deletion strains. We report that genes involved in endocytosis are required for both HU‐induced and nitrogen starvation‐induced filamentous growth. Surprisingly, no known genes involved in exocytosis are required. Despite the fact that polarized growth involves transport of vesicles to the site of growth, we failed to obtain genetic/genomic evidence that exocytosis plays an essential role in filamentous growth. A possible key role of polarized endocytosis (from the growth tip) is consistent with the proposed biological function of filamentous growth as a foraging behaviour. In addition, BUD8 that encodes the distal landmark in yeast‐form bipolar budding is required for nitrogen starvation‐induced but not HU‐induced filamentous growth. Moreover, BUD5, SPA2, PEA2 and BUD6 that regulate bipolar bud site selection do not regulate the unipolar distal budding pattern in HU‐induced filamentous growth. Copyright © 2005 John Wiley & Sons, Ltd.
Global metabolite analysis of yeast: evaluation of sample preparation methods
Authors: Villas‐Bôas Silas G. , Højer‐Pedersen Jesper , Åkesson Mats , Smedsgaard Jørn , Nielsen Jens 
Published: October 2005

AbstractSample preparation is considered one of the limiting steps in microbial metabolome analysis. Eukaryotes and prokaryotes behave very differently during the several steps of classical sample preparation methods for analysis of metabolites. Even within the eukaryote kingdom there is a vast diversity of cell structures that make it imprudent to blindly adopt protocols that were designed for a specific group of microorganisms. We have therefore reviewed and evaluated the whole sample preparation procedures for analysis of yeast metabolites. Our focus has been on the current needs in metabolome analysis, which is the analysis of a large number of metabolites with very diverse chemical and physical properties. This work reports the leakage of intracellular metabolites observed during quenching yeast cells with cold methanol solution, the efficacy of six different methods for the extraction of intracellular metabolites, and the losses noticed during sample concentration by lyophilization and solvent evaporation. A more reliable procedure is suggested for quenching yeast cells with cold methanol solution, followed by extraction of intracellular metabolites by pure methanol. The method can be combined with reduced pressure solvent evaporation and therefore represents an attractive sample preparation procedure for high‐throughput metabolome analysis of yeasts. Copyright © 2005 John Wiley & Sons, Ltd.
Activity patterns, home-range size, and habitat utilization of Sarpa salpa (Teleostei: Sparidae) in the Mediterranean Sea
Authors: Jadot C. , Donnay A. , Acolas M.L. , Cornet Y. , Bégout Anras M.L. 
Published: October 2005

AbstractAcoustic telemetry was used to record diel movement and habitat utilization of the salema (Sarpa salpa) (Teleostei: Sparidae) during three consecutive summers from 2000 to 2002 in the Calvi and Achiarina bays of Corsica in the Mediterranean Sea. A total of 18 fish was equipped with acoustic transmitters inserted in the body cavity, 13 were tracked in the Bay of Calvi (275 mm ± 26.9 LF), and 5 in Achiarina Bay (260 mm ± 33.6 LF). Two different systems were used to track the fish. The one used in the Bay of Calvi was a manual receiver and a directional hydrophone. The second system, used in Achiarina Bay, was a radio-acoustic-positioning (RAP) system that continuously monitored the movements of the fish. Fish positions were put in a geographic information system (GIS) with information on the substratum and depth. Two patterns of behaviour could be identified in the three years. Either the fish had clearly defined daytime as opposed to night-time areas of residency, characterized by different depths and substrata or the fish persistently occupied the same sites during both day and night. In the Bay of Calvi, six fish were released 1 km from the capture site. All of them showed homing ability and returned to the site within 48 h.
Host–parasite interaction of a muscle-infecting didymozoid in the Atlantic mackerel Scomber scombrus L.
Authors: Pascual S. , Abollo E. , Azevedo C. 
Published: October 2005

AbstractNumerous ribbon-like aggregations of eggs of a trematode didymozoid were found embedded in the connective tissue, mostly between the epoxial skeletal muscle fibres, of mature mackerel Scomber scombrus collected from post-recruits of the eastern stock. Egg masses contained numerous developmental stages, including pre-vitellogenous oocytes to fully embryonated eggs. Genomic DNA isolation, PCR amplification, cloning, and sequencing strongly supported the view that the eggs belong to a yet unidentified didymozoid. There was minor muscular damage to the host, namely focal distortion of host fibre architecture to accommodate the parasite, and the mild host response consisted of different stages of encapsulation. Concurrent heavy infection makes the mackerel flesh unappealing to eat, although the quality of the fish is not significantly affected and there is no public health danger.
Comparison of the efficacy of Burch colposuspension, pubovaginal sling, and tension‐free vaginal tape for stress urinary incontinence
Authors: Bai S.W. , Sohn W.H. , Chung D.J. , Park J.H. , Kim S.K. 
Published: October 2005

AbstractObjective: To compare the cure rate and confirm the clinical efficacy of the 3 most frequently performed surgical procedures for stress urinary incontinence (SUI). Methods: Between January 2001 and May 2003, 92 women with SUI were randomly assigned to undergo the Burch colposuspension (n = 33), pubovaginal sling (n = 28), or tension‐free vaginal tape (n = 31) at the Department of Obstetrics and Gynecology, Yonsei Medical Center, Seoul, Korea. Patient characteristics, urodynamic study results, cure rates at 3, 6, and 12 months, and complication rates were compared using the χ2 test. Results: There were no statistically significant differences in the cure rates initially, but after 12 months the cure rate of the pubovaginal sling procedure was found to be significantly higher than those of the tension‐free vaginal tape or Burch colposuspension procedures. Conclusion: The cure rate of the pubovaginal sling procedure was significantly higher after 1 year, but no difference in efficacy was observed between the 2 other procedures. A randomized prospective study of a larger population should be conducted.
Capsule endoscopy – comparison of two strategies of bowel preparation
Authors: NIV Y. , NIV G. , WISER K. , DEMARCO D. C. 
Published: October 2005

SummaryBackground:  Capsule endoscopy can identify lesions of the small bowel that cannot be detected by other techniques. In addition to patient safety, quality of care and cost‐efficiency, good preparation is an important factor for good visualization.Aim:  To evaluate the efficacy of oral sodium phosphate preparation.Methods:  Forty‐six consecutive patients scheduled for capsule endoscopy in two medical centres. The patients treated in Dallas were prepared by 12 h fasting (group A), and those treated in Israel were also asked to drink 45 mL of sodium phosphate with water (group B). An experienced endoscopist, blinded to the method used, graded the quality of preparation according to visual capability, and to relative durations of each grade.Results:  The quality of the preparation was poor in 35% of group A compared with 4% of group B (P = 0.023). The mean duration of good preparation with excellent visualization was 122 ± 110 min in group A and 180 ± 96 min in group B (P = 0.006). Preparation with sodium phosphate and lower patient weight were significant predictive factors for good visualization.Conclusions:  Bowel preparation offers better visualization than overnight fasting alone and is associated with fewer disturbances by intraluminal turbid fluid.
Outlet type constipation in Parkinson's disease: results of botulinum toxin treatment
Authors: CADEDDU F. , BENTIVOGLIO A. R. , BRANDARA F. , MARNIGA G. , BRISINDA G. , MARIA G. 
Published: October 2005

SummaryBackground : Constipation is one of the most common autonomic dysfunctions observed in Parkinson's disease.Aim : To investigate the efficacy of injections of botulinum toxin in improving rectal emptying in these patients.Methods : Eighteen Parkinson's disease patients with outlet constipation were included in the study. The patients were treated with type A botulinum toxin, injected into two sites on either side of the puborectalis muscle under ultrasonographic guidance.Results : Symptomatic improvement was noted in 10 patients, at 2 months evaluation. In these subjects, anorectal manometry demonstrated decreased tone during straining from 96.2 ± 17.1 to 45.9 ± 16.2 mmHg at 1 month evaluation (P = 0.00001) and to 56.1 ± 10.7 mmHg at 2 months (P = 0.00001). Pressure during straining was lower than resting anal pressure at the same times in all patients. Defecography after the treatment showed improvement in anorectal angle during straining, which increased from 99.1 ± 8.4° to 121.7 ± 12.7° (P = 0.00001) at 2 months.Conclusions : Botulinum toxin injections may be a useful treatment for Parkinson's disease patients affected by outlet‐obstruction constipation. The treatment is safe and simple. However, because the effects of the toxin wear off within 3 months of administration, repeated injections could be necessary to maintain the clinical improvement.
Prevalence and demographics of irritable bowel syndrome: results from a large web‐based survey
Authors: ANDREWS E. B. , EATON S. C. , HOLLIS K. A. , HOPKINS J. S. , AMEEN V. , HAMM L. R. , COOK S. F. , TENNIS P. , MANGEL A. W. 
Published: October 2005

SummaryBackground : Irritable bowel syndrome is a common gastrointestinal disorder, and its prevalence and demographics have been evaluated by different methodologies with varying results.Aim : To evaluate irritable bowel syndrome demographic and prevalence characteristics utilizing a web‐enabled panel.Methods : From an existing 150 000‐member panel, 31 829 individuals were randomly selected and sent screening questionnaires to evaluate irritable bowel syndrome symptoms. Individuals who agreed to participate and completed the screening questionnaire received a second questionnaire related to a diagnosis of irritable bowel syndrome, a more detailed symptom description, and additional burden of illness data.Results : Irritable bowel syndrome prevalence was 7%. Prevalence was higher in women vs. men, unmarried individuals vs. married individuals and unemployed individuals vs. employed individuals. Of those completing the second questionnaire, 51% had seen their physicians for irritable bowel syndrome symptoms in the past year and most had an episode within the past 3 months. During the past year, approximately half of the participants had used a prescription medication, and over 90% had used an over‐the‐counter medication for irritable bowel syndrome. Participants with irritable bowel syndrome demonstrated quality‐of‐life reductions relative to norms of the United States population.Conclusions : Web‐enabled data collection represents a novel tool for rapidly surveying a large population of individuals with irritable bowel syndrome symptoms.
Melatonin improves bowel symptoms in female patients with irritable bowel syndrome: a double‐blind placebo‐controlled study
Authors: LU W. Z. , GWEE K. A. , MOOCHHALLA S. , HO K. Y. 
Published: October 2005

SummaryBackground : Melatonin is involved in the regulation of gastrointestinal motility and sensation.Aim : To determine the potential therapeutic effects of melatonin in irritable bowel syndrome (IBS).Method : Seventeen female patients satisfying the Rome II criteria for IBS were randomized to receive either melatonin 3 mg nocte or identically appearing placebo 1 nocte for 8 weeks, followed by a 4‐week washout period and placebo or melatonin in the reverse order for another 8 weeks. Three validated questionnaires – the GI symptom, the sleep questionnaires and the Hospital Anxiety and Depression Scale – were used to assess symptom severity and to compute the IBS, sleep and anxiety/depression scores, respectively.Results : Improvements in mean IBS scores were significantly greater after treatment with melatonin (3.9 ± 2.6) than with placebo (1.3 ± 4.0, P = 0.037). Percent response rate, defined as percentage of subjects achieving mild‐to‐excellent improvement in IBS symptoms, was also greater in the melatonin‐treated arm (88% vs. 47%, P = 0.04). The changes in mean sleep, anxiety, and depression scores were similar with either melatonin or placebo treatment.Conclusions : Melatonin is a promising therapeutic agent for IBS. Its therapeutic effect is independent of its effects on sleep, anxiety or depression.