bluuebunny/crossref_metadata_2025_split huggingface dataset:
HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence
Authors: Lin Hsin-Nan , Chang Jia-Ming , Wu Kuen-Pin , Sung Ting-Yi , Hsu Wen-Lian 
Published: June 2005

Abstract
Motivation: In our previous approach, we proposed a hybrid method for protein secondary structure prediction called HYPROSP, which combined our proposed knowledge-based prediction algorithm PROSP and PSIPRED. The knowledge base constructed for PROSP contains small peptides together with their secondary structural information. The hybrid strategy of HYPROSP uses a global quantitative measure, match rate, to determine whether PROSP or PSIPRED is to be used for the prediction of a target protein. HYPROSP made slight improvement of Q3 over PSIPRED because PROSP predicted well for proteins with match rate &gt;80%. As the portion of proteins with match rate &gt;80% is quite small and as the performance of PSIPRED also improves, the advantage of HYPROSP is diluted. To overcome this limitation and further improve the hybrid prediction method, we present in this paper a new hybrid strategy HYPROSP II that is based on a new quantitative measure called local match rate.
Results: Local match rate indicates the amount of structural information that each amino acid can extract from the knowledge base. With the local match rate, we are able to define a confidence level of the PROSP prediction results for each amino acid. Our new hybrid approach, HYPROSP II, is proposed as follows: for each amino acid in a target protein, we combine the prediction results of PROSP and PSIPRED using a hybrid function defined on their respective confidence levels. Two datasets in nrDSSP and EVA are used to perform a 10-fold cross validation. The average Q3 of HYPROSP II is 81.8% and 80.7% on nrDSSP and EVA datasets, respectively, which is 2.0% and 1.1% better than that of PSIPRED. For local structures with match rate &gt;80%, the average Q3 improvement is 4.4% on the nrDSSP dataset. The use of local match rate improves the accuracy better than global match rate. There has been a long history of attempts to improve secondary structure prediction. We believe that HYPROSP II has greatly utilized the power of peptide knowledge base and raised the prediction accuracy to a new high. The method we developed in this paper could have a profound effect on the general use of knowledge base techniques for various predictionalgorithms.
Availability: The Linux executable file of HYPROSP II, as well as both nrDSSP and EVA datasets can be downloaded from http://bioinformatics.iis.sinica.edu.tw/HYPROSPII/
Contact: hsu@iis.sinica.edu.tw
Modelling biological complexity: a physical scientist's perspective
Authors: Coveney Peter V , Fowler Philip W 
Published: June 2005

We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter.The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view.
Effect of CYP2C19 polymorphism on the safety and efficacy of omeprazole in Japanese patients with recurrent reflux oesophagitis
Authors: Ohkusa T. , Maekawa T. , Arakawa T. , Nakajima M. , Fujimoto K. , Hoshino E. , Mitachi Y. , Hamada S. , Mine T. , Kawahara Y. , Nagai T. , Aoyama N. , Yoshida N. , Tadokoro K. , Chida N. , Konda Y. , Seno H. , Shimatani T. , Inoue M. , Sato N. 
Published: June 2005

SummaryBackground : The polymorphic enzyme cytochrome P450 2C19 affects omeprazole metabolism. This influence on metabolism might affect serum gastrin levels, and safety, during long‐term treatment of reflux oesophagitis.Aim : To examine the relationship between cytochrome P450 2C19 genotype and the safety profile of long‐term omeprazole treatment.Methods : A total of 119 Japanese patients with recurrent reflux oesophagitis underwent cytochrome P450 2C19 genotyping prior to receiving daily omeprazole 10 mg or 20 mg for 6–12 months, during which adverse event frequency, serum gastrin levels and endoscopic findings were monitored.Results : The incidences of adverse events, serious adverse events and adverse events leading to withdrawal did not differ between homozygous extensive metabolizer (n = 46), heterozygous extensive metabolizer (n = 53) or poor metabolizer (n = 20) groups. In all genotype groups, serum gastrin increased during the first 3 months of dosing but stabilized thereafter. No significant differences were seen either in the rate of reflux oesophagitis healing or symptom improvement among genotype groups.Conclusions : Long‐term treatment with omeprazole was well‐tolerated in Japanese patients, irrespective of their cytochrome P450 2C19 metabolic genotype, indicating that dose adjustment depending on metabolic genotype is not required during treatment with omeprazole.
The effect of rabeprazole on regional gastric acidity and the postprandial cardia/gastro‐oesophageal junction acid layer in normal subjects: a randomized, double‐blind, placebo‐controlled study
Authors: Vo L. , Simonian H. P. , Doma S. , Fisher R. S. , Parkman H. P. 
Published: June 2005

SummaryBackground : Postprandial intragastric acidity is not uniform. Postprandial proximal gastric acid pockets have been described in the present study.Aim : To determine the effects of rabeprazole on regional intragastric acidity and proximal acid pockets.Methods : Ten normal subjects underwent two 8‐day oral dosing regimens with placebo or rabeprazole 20 mg each morning in a randomized, double‐blind protocol. Oesophago‐gastric pH monitoring was performed on days 1 and 8.Results : Rabeprazole increased fasting and postprandial gastric pH to above 4 in each area of the stomach on days 1 and 8. With placebo, acid pockets were identified at the cardia/gastro‐oesophageal junction in 62 and 50 of 150 pull‐throughs on days 1 and 8, respectively. Acid pockets were detected postprandially 3.1 ± 0.2–5.8 ± 0.1 cm below the proximal border of the lower oesophageal sphincter with a mean pH drop from 4.6 ± 0.1 to 1.5 ± 0.1. Rabeprazole decreased the number of acid pockets to 30 and 27 on days 1 and 8, respectively. Rabeprazole also decreased their length and magnitude of the pH drop.Conclusions : Rabeprazole increased intragastric pH on day 1 and 8 and maintained an elevated pH during and after meals. Postprandial acid pockets, identified in the region of the cardia/gastro‐oesophageal junction area postprandially, were decreased in number, length and magnitude by rabeprazole.
Systematic review: the efficacy of intermittent and on‐demand therapy with histamine H2‐receptor antagonists or proton pump inhibitors for gastro‐oesophageal reflux disease patients
Authors: Zacny J. , Zamakhshary M. , Sketris I. , Veldhuyzen van Zanten S. 
Published: June 2005

SummaryAim : To perform a systematic review on the efficacy of intermittent and on‐demand therapy with either histamine H2‐receptor antagonists or proton pump inhibitors for patients with erosive oesophagitis or symptomatic heartburn.Method : We conducted randomized‐controlled trials of non‐continuous therapy in gastro‐oesophageal reflux disease patients.Results : Fourteen studies met inclusion criteria. Because of variation in outcome measures statistical pooling of results was not possible. Results were analysed qualitatively. Four studies evaluated intermittent therapy of treatment 3 days a week with omeprazole 20 mg or daily with ranitidine which were not efficacious compared to a daily proton pump inhibitor. Famotidine 10 and 20 mg, ranitidine 75 mg and cimetidine 200 mg were efficacious in five on‐demand studies for relief of symptomatic heartburn episodes. In three of four studies, evaluating only non‐erosive (endoscopy‐negative) gastro‐oesophageal reflux disease patients, esomeprazole 20 and 40 mg and omeprazole 10 and 20 mg a day were efficacious using willingness to continue as an endpoint. Lansoprazole 30 mg and omeprazole 20 mg maintained symptom control in 60–70% of healed oesophagitis patients.Conclusions : Intermittent proton pump inhibitor or H2‐receptor antagonist therapy is not effective in maintaining control in oesophagitis patients. H2‐receptor antagonists are effective for relief of heartburn episodes. On‐demand proton pump inhibitor therapy may work in a proportion of non‐erosive gastro‐oesophageal reflux disease patients.
Abnormal breath tests to lactose, fructose and sorbitol in irritable bowel syndrome may be explained by small intestinal bacterial overgrowth
Authors: Nucera G. , Gabrielli M. , Lupascu A. , Lauritano E. C. , Santoliquido A. , Cremonini F. , Cammarota G. , Tondi P. , Pola P. , Gasbarrini G. , Gasbarrini A. 
Published: June 2005

SummaryBackground : Small intestinal bacterial overgrowth and sugar malabsorption (lactose, fructose, sorbitol) may play a role in irritable bowel syndrome. The lactulose breath test is a reliable and non‐invasive test for the diagnosis of small intestinal bacterial overgrowth. The lactose, fructose and sorbitol hydrogen breath tests are widely used to detect specific sugar malabsorption.Aim : To assess the extent to which small intestinal bacterial overgrowth may influence the results of hydrogen sugar breath tests in irritable bowel syndrome patients.Methods : We enrolled 98 consecutive irritable bowel syndrome patients. All subjects underwent hydrogen lactulose, lactose, fructose and sorbitol hydrogen breath tests. Small intestinal bacterial overgrowth patients were treated with 1‐week course of antibiotics. All tests were repeated 1 month after the end of therapy.Results : A positive lactulose breath test was found in 64 of 98 (65%) subjects; these small intestinal bacterial overgrowth patients showed a significantly higher prevalence of positivity to the lactose breath test (P < 0.05), fructose breath test (P < 0.01) and sorbitol breath test (P < 0.01) when compared with the small intestinal bacterial overgrowth‐negatives. Small intestinal bacterial overgrowth eradication, as confirmed by negative lactulose breath test, caused a significant reduction in lactose, fructose and sorbitol breath tests positivity (17% vs. 100%, 3% vs. 62%, and 10% vs. 71% respectively: P < 0.0001).Conclusions : In irritable bowel syndrome patients with small intestinal bacterial overgrowth, sugar breath tests may be falsely abnormal. Eradication of small intestinal bacterial overgrowth normalizes sugar breath tests in the majority of patients. Testing for small intestinal bacterial overgrowth should be performed before other sugar breath tests tests to avoid sugar malabsorption misdiagnosis.
Occult hepatitis B virus infection in dialysis patients: a multicentre survey
Authors: Fabrizi F. , Messa P. G. , Lunghi G. , Aucella F. , Bisegna S. , Mangano S. , Villa M. , Barbisoni F. , Rusconi E. , Martin P. 
Published: June 2005

SummaryBackground : The epidemiology and clinical significance of occult hepatitis B virus infection (serum hepatitis B surface antigen‐negative patients with detectable hepatitis B virus viraemia in serum) remains controversial with only limited information about its prevalence in patients on long‐term dialysis.Aim : To address the epidemiology of occult HBV infection in a large cohort of dialysis patients.Methods : We screened a large cohort (n = 585) of Italian chronic dialysis patients; from this population, a group of hepatitis B virus surface antigen seronegative patients (n = 213) was tested by Amplicor hepatitis B virus Monitor Test to detect hepatitis B virus viraemia (hepatitis B virus‐DNA) in serum.Results : Occult hepatitis B virus infection was absent (zero of 213 = 0%). Persistent hepatitis B virus surface antigen carriage was less frequent than anti‐hepatitis B virus core antibody (anti‐hepatitis B core antigen) seropositive status in this study group [1.88% (11 of 585) vs. 36% (216 of 585), P = 0.0001]. No dialysis patients seropositive for anti‐hepatitis B core antibody in serum (zero of 123 = 0%) had detectable hepatitis B virus‐DNA by polymerase chain reaction technology. No significant association between abnormal biochemical liver tests and serum anti‐hepatitis B core antibody was noted in our population. Nominal logistic regression analysis demonstrated an independent and significant relationship between anti‐HCV antibody and anti‐hepatitis B virus core antibody in serum (Wald chi‐square 16.06, P = 0.0001). The rate of seropositive patients for anti‐hepatitis B virus core antibody was higher among study patients than controls with normal renal function [36.9% (216 of 585) vs. 21.4% (59 of 275), P = 0.0001]; this difference partially persisted after correction for demographic parameters, and viral markers.Conclusion : In conclusion, occult hepatitis B virus was absent in our study group. Anti‐hepatitis B core antibody was significantly related to presence of anti‐HCV antibody supporting shared modes of transmission. Clinical studies based on molecular biology techniques provided with higher sensitivity are planned.
Empirical treatment for the management of patients presenting with uninvestigated reflux symptoms: a prospective study in an Asian primary care population
Authors: Ho K. Y. , Gwee K. A. , Khor C. J. , Selamat D. S. , Wai C. T. , Yeoh K. G. 
Published: June 2005

SummaryBackground : Data on Asian patients who present with reflux symptoms to their primary care physicians are limited.Aim : To determine whether empirical therapy without endoscopy is appropriate for patients who present to their primary care physicians with uninvestigated reflux symptoms without alarm symptoms.Method : Forty‐seven patients presenting with uninvestigated, dominant reflux symptoms but without alarm features to their primary care physicians underwent endoscopy within 2 weeks of referral. Their endoscopic findings were compared with those of 162 primary care patients presenting with uninvestigated dominant dyspepsia. All patients, except those with ulcers, were treated with esomeprazole 20 mg b.d. for 2 weeks. Their treatment response was assessed at 2 weeks using a symptom score.Results : Among patients with dominant reflux symptoms, 14 (30%) had erosive oesophagitis. No other clinically significant endoscopic findings were detected among them. In contrast, erosive oesophagitis and peptic ulcer were found in 13 (8%, P < 0.001 vs. reflux group), and 12 (7%, P = 0.06 vs. reflux group), respectively, of patients with dominant dyspepsia. Thirty‐seven of forty‐five (82%) of those with dominant reflux symptoms and 109 of 139 (78%; P = N.S. vs. reflux group) of those with dominant dyspepsia reported ≥50% resolution of symptoms after esomeprazole treatment.Conclusions : Empirical proton pump inhibitor without endoscopy is reasonable for uninvestigated patients who present to primary care physicians with dominant reflux symptoms.
Identification of a putative voltage‐gated Ca2+ channel as a key regulator of elicitor‐induced hypersensitive cell death and mitogen‐activated protein kinase activation in rice
Authors: Kurusu Takamitsu , Yagala Toshikazu , Miyao Akio , Hirochika Hirohiko , Kuchitsu Kazuyuki 
Published: June 2005

SummaryElicitor‐triggered transient membrane potential changes and Ca2+ influx through the plasma membrane are thought to be important during defense signaling in plants. However, the molecular bases for the Ca2+ influx and its regulation remain largely unknown. Here we tested effects of overexpression as well as retrotransposon (Tos17)‐insertional mutagenesis of the rice two‐pore channel 1 (OsTPC1), a putative voltage‐gated Ca2+‐permeable channel, on a proteinaceous fungal elicitor‐induced defense responses in rice cells. The overexpressor showed enhanced sensitivity to the elicitor to induce oxidative burst, activation of a mitogen‐activated protein kinase (MAPK), OsMPK2, as well as hypersensitive cell death. On the contrary, a series of defense responses including the cell death and activation of the MAPK were severely suppressed in the insertional mutant, which was complemented by overexpression of the wild‐type gene. These results suggest that the putative Ca2+‐permeable channel determines sensitivity to the elicitor and plays a role as a key regulator of elicitor‐induced defense responses, activation of MAPK cascade and hypersensitive cell death.
Characterization of two GL8 paralogs reveals that the 3‐ketoacyl reductase component of fatty acid elongase is essential for maize (Zea mays L.) development
Authors: Dietrich Charles R. , Perera M. Ann D. N. , D. Yandeau‐Nelson Marna , Meeley Robert B. , Nikolau Basil J. , Schnable Patrick S. 
Published: June 2005

SummaryPrior analyses established that the maize (Zea mays L.) gl8a gene encodes 3‐ketoacyl reductase, a component of the fatty acid elongase required for the biosynthesis of very long chain fatty acids (VLCFAs). A paralogous gene, gl8b, has been identified that is 96% identical to gl8a. The gl8a and gl8b genes map to syntenic chromosomal regions, have similar, but not identical, expression patterns, and encode proteins that are 97% identical. Both of these genes are required for the normal accumulation of cuticular waxes on seedling leaves. The chemical composition of the cuticular waxes from gl8a and gl8b mutants indicates that these genes have at least overlapping, if not redundant, functions in cuticular wax biosynthesis. Although gl8a and gl8b double mutant kernels have endosperms that cannot be distinguished from wild‐type siblings, these kernels are non‐viable because their embryos fail to undergo normal development. Double mutant kernels accumulate substantially reduced levels of VLCFAs. VLCFAs are components of a variety of compounds, for example, cuticular waxes, suberin, and sphingolipids. Consistent with their essential nature in yeast, the accumulation of the ceramide moiety of sphingolipids is substantially reduced and their fatty acid composition altered in gl8a and gl8b double mutant kernels relative to wild‐type kernels. Hence, we hypothesize that sphingolipids or other VLCFA‐containing compounds are essential for normal embryo development.
Experimental determination of proline hydroxylation and hydroxyproline arabinogalactosylation motifs in secretory proteins
Authors: Shimizu Masami , Igasaki Tomohiro , Yamada Makiko , Yuasa Koji , Hasegawa Jyunko , Kato Tetsuji , Tsukagoshi Hironaka , Nakamura Kenzo , Fukuda Hiroo , Matsuoka Ken 
Published: June 2005

SummaryMany secretory and several vacuolar proteins in higher plants contain hydroxylated proline residues. In many cases, hydroxyprolines in proteins are glycosylated with either arabinogalactan or oligoarabinose. We have previously shown that a sporamin precursor is O‐glycosylated at the hydroxylated proline 36 residue with an arabinogalactan‐type glycan when this protein is expressed in tobacco BY‐2 cells (Matsuoka et al., 1995). Taking advantage of the fact that this is the only site of proline hydroxylation and glycosylation in sporamin, we analyzed the amino acid requirement for proline hydroxylation and arabinogalactosylation. We expressed several deletion constructs and many amino acid substitution mutants in tobacco cells and analyzed glycosylation and proline hydroxylation of the expressed sporamins. Hydroxylation of a proline residue requires the five amino acid sequence [AVSTG]–Pro–[AVSTGA]–[GAVPSTC]–[APS or acidic] (where Pro is the modification site) and glycosylation of hydroxyproline (Hyp) requires the seven amino acid sequence [not basic]–[not T]–[neither P, T, nor amide]–Hyp–[neither amide nor P]–[not amide]–[APST], although charged amino acids at the −2 position and basic amide residues at the +1 position relative to the modification site seem to inhibit the elongation of the arabinogalactan side chain. Based on the combination of these two requirements, we concluded that the sequence motif for efficient arabinogalactosylation, including the elongation of the glycan side chain, is [not basic]–[not T]–[AVSG]–Pro–[AVST]–[GAVPSTC]–[APS].
White‐core endosperm floury endosperm‐4 in rice is generated by knockout mutations in the C4‐type pyruvate orthophosphate dikinase gene (OsPPDKB)
Authors: Kang Hong‐Gyu , Park Sunhee , Matsuoka Makoto , An Gynheung 
Published: June 2005

SummaryWe have isolated a floury endosperm‐4 (flo4) rice mutant with a floury‐white endosperm but a normal outer portion. Scanning electron microscopic analysis revealed that this abnormal endosperm consisted of loosely packed starch granules. The mutant phenotype was generated by T‐DNA insertion into the fifth intron of the OsPPDKB gene encoding pyruvate orthophosphate dikinase (PPDK). Plants containing flo4‐1 produced no OsPPDKB transcript or the OsPPDKB protein in their developing kernels and leaves. We obtained two additional alleles, flo4‐2 and flo4‐3, that also showed the same white‐core endosperm phenotype. The flo4 kernels weighed about 6% less than wild‐type ones. Starch contents in both kernel types were similar, but the total protein content was slightly higher in the mutant kernels. Moreover, lipid contents were significantly increased in the flo4 kernels. Expression analyses demonstrated that the cytosolic mRNA of OsPPDKB was induced in the reproductive organs after pollination, and greatly increased until about 10 days after fertilization. This mRNA was localized mainly in the endosperm, aleurone, and scutellum of the developing kernel. Our results suggest that cytosolic PPDK functions in rice to modulate carbon metabolism during grain filling.