bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of structural features of monomeric helical peptides designed with a genetic algorithm
Authors: Zhang Wuming , Loughran Micheal G. , Kanna Shin‐ichi , Yano Kazuyoshi , Ikebukuro Kazunori , Yokobayashi Yohei , Kuroda Reiko , Karube Isao 
Published: October 2004

AbstractA genetic algorithm (GA)‐based strategy to dissect the determinants of peptide folding into α‐helix was developed. The structural information of helical peptides was obtained with respect to patterns of sequence variability. In many previously reported studies the intrinsic α‐helical propensities of amino acids although sequence‐dependent are apparently independent of the amino acid position. In this research, monomeric helical peptides selected from possible sequences produced by a GA‐chemical synthesis were analyzed to identify possible influential structural features. These hexadeca‐peptides were obtained after four successive generations. A total of 128 synthetic peptides were evaluated via circular dichroism (CD) measurements in aqueous solution, while the mean ellipticity at 222 nm confirmed the monomeric state of the peptides. The results presented here show that our GA‐based strategy may be useful in the design of proteins with increased α‐helix content. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Efficient minimization of angle‐dependent potentials for polypeptides in internal coordinates
Authors: Wedemeyer William J. , Baker David 
Published: October 2004

AbstractAngular potentials play an important role in the refinement of protein structures through angle‐dependent restraints (e.g., those determined by cross‐correlated relaxations, residual dipolar couplings, and hydrogen bonds). Analytic derivatives of such angular potentials with respect to the dihedral angles of proteins would be useful for optimizing such restraints and other types of angular potentials (i.e., such as we are now introducing into protein structure prediction) but have not been described. In this article, analytic derivatives are calculated for four types of angular potentials and integrated with the efficient recursive derivative calculation methods of Gō and coworkers. The formulas are implemented in publicly available software and illustrated by refining a low‐resolution protein structure with idealized vector‐angle, dipolar‐coupling, and hydrogen‐bond restraints. The method is now being used routinely to optimize hydrogen‐bonding potentials in ROSETTA. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Thinking differently about cultural diversity: Using postcolonial theory to (re)read science education
Authors: Carter Lyn 
Published: October 2004

AbstractThis paper makes use of postcolonial theory to think differently about aspects of cultural diversity within science education. It briefly reviews some of the increasing scholarship on cultural diversity, and then describes the genealogy and selected key themes of postcolonial theory. Postcolonial theory as oppositional or deconstructive reading practice is privileged, and its practical application illustrated by using some of these key ideas to (re)read Gloria Snively and John Corsiglia's (2001) article “Discovering indigenous science: implications for science education” and their rejoinder, from the special issue of Science Education (Vol. 85, pp. 6–34) on multiculturalism and science education. While many would regard the expressed views on diversity, inclusivity, multiculturalism, and sustainability to be just and equitable, postcolonial analysis of the texts reveals subtle and lingering referents that unwittingly work against the very attitudes Snively and Corsiglia (2001) seek to promote. Such postcolonial analyses open up thinking about the material and cultural conditions in which science education is produced, circulated, interpreted, and enacted. They also privilege a unique methodology already prominent in academic inquiry that is yet to be well explored within science education. Finally, I conclude this paper with some general comments regarding postcolonialism and the science education scholarship on cultural diversity. © 2004 Wiley Periodicals, Inc. Sci Ed 88:819–836, 2004
Deliberate learning in corporate acquisitions: post‐acquisition strategies and integration capability in U.S. bank mergers
Authors: Zollo Maurizio , Singh Harbir 
Published: October 2004

AbstractThis paper introduces a knowledge‐based view of corporate acquisitions and tests the post‐acquisition consequences on performance of integration decisions and capability‐building mechanisms. In our model, the acquiring firm decides both how much to integrate the acquired firm and the extent to which it replaces this firm's top management team. It can also learn to manage the post‐acquisition integration process by tacitly accumulating acquisition experience and explicitly codifying it in manuals, systems, and other acquisition‐specific tools. Using a sample of 228 acquisitions in the U.S. banking industry, we find that knowledge codification strongly and positively influences acquisition performance, while experience accumulation does not. Furthermore, increasing levels of post‐acquisition integration strengthen the positive effect of codification. Finally, the level of integration between the two merged firms significantly enhances performance, while replacing top managers in the acquired firm negatively impacts performance, all else being equal. Implications are drawn for both organizational learning theory and a knowledge‐based approach to corporate strategy research. Copyright © 2004 John Wiley & Sons, Ltd.
PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
Authors: Gardy J. L. , Laird M. R. , Chen F. , Rey S. , Walsh C. J. , Ester M. , Brinkman F. S. L. 
Published: October 2004

Abstract
Motivation: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program's predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb's coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization.
Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size.
Availability: Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License.
Contact: psort-mail@sfu.ca, brinkman@sfu.ca
Supplementary information: http://www.psort.org/psortb/supplementaryinfo.html
Comparison of different melting temperature calculation methods for short DNA sequences
Authors: Panjkovich Alejandro , Melo Francisco 
Published: October 2004

Abstract
Motivation: The overall performance of several molecular biology techniques involving DNA/DNA hybridization depends on the accurate prediction of the experimental value of a critical parameter: the melting temperature Tm. Till date, many computer software programs based on different methods and/or parameterizations are available for the theoretical estimation of the experimental Tm value of any given short oligonucleotide sequence. However, in most cases, large and significant differences in the estimations of Tm were obtained while using different methods. Thus, it is difficult to decide which Tm value is the accurate one. In addition, it seems that most people who use these methods are unaware about the limitations, which are well described in the literature but not stated properly or restricted the inputs of most of the web servers and standalone software programs that implement them.
Results: A quantitative comparison on the similarities and differences among some of the published DNA/DNA Tm calculation methods is reported. The comparison was carried out for a large set of short oligonucleotide sequences ranging from 16 to 30 nt long, which span the whole range of CG-content. The results showed that significant differences were observed in all the methods, which in some cases depend on the oligonucleotide length and CG-content in a non-trivial manner. Based on these results, the regions of consensus and disagreement for the methods in the oligonucleotide feature space were reported. Owing to the lack of sufficient experimental data, a fair and complete assessment of accuracy for the different methods is not yet possible. Inspite of this limitation, a consensus Tm with minimal error probability was calculated by averaging the values obtained from two or more methods that exhibit similar behavior to each particular combination of oligonucleotide length and CG-content class. Using a total of 348 DNA sequences in the size range between 16mer and 30mer, for which the experimental Tm data are available, we demonstrated that the consensus Tm is a robust and accurate measure. It is expected that the results of this work would be constituted as a useful set of guidelines to be followed for the successful experimental implementation of various molecular biology techniques, such as quantitative PCR, multiplex PCR and the design of optimal DNA microarrays.
Availability: A binary software distribution to calculate the consensus Tm described in this work for thousands of oligonucleotides simultaneously for the LINUX operating system is freely available upon request to the authors or from our website http://protein.bio.puc.cl/melting-temperatures.html
Contact: fmelo@bio.puc.cl
Supplementary information: The large set of oligonucleotides, the detailed results of the comparative and accuracy benchmarks, and hundreds of comparative graphs generated during this work are available at our website http://protein.bio.puc.cl/melting-temperatures.html
ATP Depletion Of Tubular Cells Causes Dissociation of the Zonula Adherens and Nuclear Translocation of β-Catenin and LEF-1
Authors: Price Valerie R. , Reed Christine A. , Lieberthal Wilfred , Schwartz John H. 
Published: October 2004

ABSTRACT.
This study examined the events associated with the reversible disruption of the structural and functional integrity of the zonula occludens (ZA) induced by ATP depletion of renal tubular cells. It shows that loss of the ZA after ATP depletion is associated with the withdrawal of E-cadherin, α-catenin, and β-catenin, probably as intact cadherin-catenin complexes from the basolateral membrane of tubular cells. The relative amounts of all three proteins increased in the Triton X-100–insoluble fraction of cell lysates and decreased in the Triton X-100–soluble pool. These changes were reversed with repletion of cell ATP. It is additionally shown that ATP depletion induces nuclear translocation of β-catenin and T cell factor (TCF)/lymphoid enhancer factor–1 (LEF-1), a transcriptional factor with which β-catenin associates. The redistribution of the ZA proteins as intact E-cadherin-catenin complexes from the plasma membrane facilitates the rapid recovery of the ZA after sublethal ischemic injury. The translocation of β-catenin and TCF/LEF-1 to the nucleus indicates that ATP depletion may activate the wnt/wingless signal transduction pathway. Thus, entirely novel evidence is provided that both of the known roles of β-catenin, as a structural part of the ZA and as a component of the wnt/wingless pathway, play a role after sublethal ischemic injury to tubular cells. It is also speculated that the nuclear translocation of β-catenin and TCF/LEF-1 modulates gene expression after ischemic injury and may contribute to events necessary for renal regeneration and repair after ischemic injury.
The Hypertrophic Effect of Transforming Growth Factor-β is Reduced in the Absence of Cyclin-Dependent Kinase-Inhibitors p21 and p27
Authors: Monkawa Toshiaki , Hiromura Keiju , Wolf Gunter , Shankland Stuart J 
Published: October 2004

ABSTRACT.
Transforming growth factor-β (TGF-β) has both antiproliferative and hypertrophic effects on mesangial cells (MC). However, it is not known if these processes are independent or if they share common signaling pathways. Proliferation and hypertrophy are regulated by specific cell-cycle regulatory proteins, where the cyclin-dependent kinase (CDK) inhibitors inhibit target cyclin-CDK complexes. This study examined whether the growth regulatory effects of TGF-β were determined by the CDK inhibitors p21 and p27. Accordingly, cultured MC from wild type (+/+) and single and double null (−/−) p21 and p27 mice were grown in 5% serum in the presence or absence of TGF-β1 (2 ng/ml). Proliferation ([3H]-thymidine incorporation, cell number, cell cycle) and hypertrophy ([3H]-leucine incorporation, total protein content, forward light scatter) were measured after 24 h, 48 h, and 96 h. TGF-β inhibited proliferation in +/+ and p21/p27 double −/− MC to a similar extent. TGF-β induced hypertrophy in +/+ MC (18.0% increase at 48 h), and to lesser extent in p21 −/− (12.8%) and p27 −/− MC (11.5%) measured by forward light scatter analysis. In p21/p27 double −/−, the hypertrophic effects of TGF-β were significantly reduced (3.9% at 48 h). Similar results were obtained by measuring hypertrophy by total protein and [3H]-leucine incorporation. In conclusion, the CDK inhibitors p21 and p27 are not required for the antiproliferative effects of TGF-β. However, the hypertrophic growth effects of TGF-β are reduced in the absence of both p21 and p27. These data suggest that the regulation of the antiproliferative and hypertrophic effects of TGF-β may be distinct processes.
Trends in Anemia Management among US Hemodialysis Patients
Authors: Coladonato Joseph A. , Frankenfield Diane L. , Reddan Donal N. , Klassen Preston S. , Szczech Lynda A. , Johnson Curtis A. , Owen William F. 
Published: October 2004

ABSTRACT.
This study was undertaken to describe the relationship between hematocrit (Hct) and changes in the prescribed dose of erythropoietin (EPO) as well as selected patient and process care measures across annual national samples of hemodialysis patients from 1994 to 1998. This study uses the cohorts identified in the ESRD Core Indicators Project, random samples of 6181, 6241, 6364, 6634, and 7660 patients, stratified by ESRD Networks drawn for each year from 1994 to 1998. Patient demographic and clinical information was collected from October to December for each year. Surrogates of iron stores and patterns of iron and EPO administration were profiled from 1996 to 1998. Multivariable stepwise linear regression analyses were performed to adjust for potential confounding variables and to identify independent variables associated with Hct and EPO dose. Mean Hct and EPO dose increased each year from 31.1 ± 5.2% to 34.1 ± 3.7% and from 58.2 ± 41.8 U/kg to 68.2 ± 55.0 U/kg, respectively (P = 0.0001). Increasing Hct was positively associated with male gender, more years on dialysis, older age, higher urea reduction ratio and transferrin saturation, prescription of intravenous iron, and lower ferritin and EPO dose in multivariable models (all P = 0.0001). Male gender, older age, diabetes, higher Hct, and increasing weight, urea reduction ration, and transferrin saturation were associated with lower EPO doses (all P < 0.01). Conversely, intravenous EPO and iron were associated with higher prescribed EPO doses (all P = 0.0001). Although increasing Hct is associated with decreasing EPO dose at the patient level, the increase in Hct seen across years among the cohorts of hemodialysis patients in the United States has been associated with increasing doses of EPO at the population level.
Preemptive Kidney Transplantation
Authors: Kasiske Bertram L. , Snyder Jon J. , Matas Arthur J. , Ellison Mary D. , Gill John S. , Kausz Annamaria T. 
Published: October 2004

ABSTRACT.
It remains unclear whether preemptive transplantation is beneficial, and if so, who benefits. A total of 38,836 first, kidney-only transplants between 1995 and 1998 were retrospectively studied. A surprising 39% of preemptive transplants were from cadaver donors, and the proportions of cadaver donor transplants that were preemptive changed little, from 7.3% in 1995 to 7.7% in 1998. Preemptive transplants using cadaver donors were more likely among recipients aged 0 to 17 yr versus 18 to 29 yr (odds ratio [OR], 2.48; 95% confidence interval [CI], 1.94 to 3.17), white versus black (OR, 2.33; 95% CI, 2.03 to 2.68), able to work versus unable to work (OR, 1.42; 95% CI, 1.26 to 1.61), covered by private insurance versus Medicare (OR, 4.77; 95% CI, 4.26 to 5.32), or recipients with a college degree versus no college degree (OR, 1.34; 95% CI, 1.17 to 1.54). Preemptive transplants were less likely for Hispanics versus non-Hispanics (OR, 0.57; 95% CI, 0.50 to 0.67), patients with type 2 versus type 1 diabetes (OR, 0.76; 95% CI, 0.61 to 0.96), and for 2 to 5 HLA mismatches compared with 0 HLA mismatches (OR range, 0.77 to 0.82). In adjusted Cox proportional hazards analysis, the relative risk of graft failure for preemptive transplantation was 0.75 (0.67 to 0.84) among 25,758 cadaver donor transplants and 0.73 (0.64 to 0.83) among 13,078 living donor transplants, compared with patients who received a transplant after already being on dialysis. Preemptive transplantation was associated with a reduced risk of death: 0.84 (0.72 to 0.99) for cadaver donor transplants and 0.69 (0.56 to 0.85) for living donor transplants. Thus, preemptive transplantation, which is associated with improved patient and graft survival, is less common among racial minorities, those who have less education, and those who must rely on Medicare for primary payment. Alterations in the payment system, emphasis on early referral, and changes in cadaver kidney allocation could increase the number of patients who benefit from preemptive transplantation.
Increased Oxidative Damage to Peripheral Blood Leukocyte DNA in Chronic Peritoneal Dialysis Patients
Authors: Tarng Der-Cherng , Wen Chen Tzen , Huang Tung-Po , Chen Chiu-Lan , Liu Tsung-Yun , Wei Yau-Huei 
Published: October 2004

ABSTRACT.
This study focuses on the extent of oxidative DNA damage in peripheral blood leukocytes of chronic peritoneal dialysis (CPD) patients. 8-Hydroxy 2′-deoxyguanosine (8-OHdG) contents in peripheral leukocyte DNA were measured by an HPLC-electrochemical detection method in 24 age- and sex-matched healthy subjects, 22 nondialyzed patients with advanced renal failure, and 42 CPD patients. Mean 8-OHdG content was the highest in CPD patients, followed by the nondialyzed patients, and then by the healthy subjects (19.4 versus 11.9 versus 8.3/106 dG; ANOVA P < 0.001). In nondialyzed subjects, peripheral leukocyte 8-OHdG contents inversely correlated with renal creatinine clearance (r = −0.772; P < 0.001). Deficiency of blood antioxidants in CPD and nondialyzed patients was expressed by the lower plasma levels of ascorbate, cholesterol-standardized α-tocopherol and whole-blood reduced glutathione, and the higher levels of whole-blood oxidized glutathione as compared with healthy subjects (ANOVA P < 0.05). Mean serum ferritin and iron levels and transferrin saturation were higher in the CPD patients than those in the nondialyzed patients and controls (ANOVA P < 0.05). Flow cytometric analyses of intracellular reactive oxygen species production of peripheral leukocytes showed that spontaneous production by granulocytes, as well as phorbol-12-myristate-13-acetate (PMA)–induced production by granulocytes, lymphocytes and monocytes, were the highest from CPD patients, followed by nondialyzed patients, and then by the healthy subjects (ANOVA P < 0.05). Forward stepwise multiple regression disclosed that uremia, PD treatment, spontaneous and PMA-induced reactive oxygen species production in leukocytes, and serum iron were the independent determinants of peripheral leukocyte 8-OHdG content (R2
= 0.769; P < 0.001). In conclusion, profound increased 8-OHdG levels in peripheral leukocyte DNA occur in the course of chronic renal failure, gradually increase with its progression, and are further exacerbated by PD treatment.
Transcription Factor IRF-1 in Kidney Transplants Mediates Resistance to Graft Necrosis during Rejection
Authors: Afrouzian Marjan , Ramassar Vido , Urmson Joan , Zhu Lin-Fu , Halloran Philip F. 
Published: October 2004

ABSTRACT.
In many circumstances kidney transplants remain viable despite extensive inflammation, permitting rejection episodes to be reversed. The mechanisms by which the kidney resists host effector mechanisms are not known. In mouse kidney transplants, resistance requires interferon-γ (IFN-γ), which acts on the graft to protect the graft from necrosis during the first days of rejection as well as inducing major histocompatibility complex (MHC) expression. Because some effects of IFN-γ are mediated by transcription factor IRF-1, the role of IRF-1 in the donor tissue early phases of rejection of mouse kidney allografts was studied. H-2b kidneys were transplanted from mice with wild-type IRF-1 genes (WT) or mice with disrupted IRF-1 genes (IRF-1KO) into CBA (H-2k) recipients. At day 5 and day 7, IRF-1KO and WT kidneys were functioning despite typical rejection pathology: interstitial infiltration and tubulitis. However, function deteriorated rapidly in rejecting IRF-1KO allografts, associated with widespread epithelial necrosis, peritubular capillary congestion, glomerulitis, and fibrin thrombi in small veins by day 7. At day 21, WT kidneys were viable despite severe tubulitis and arteritis, whereas IRF-1KO kidneys showed massive necrosis of the epithelium despite patent large vessels. Compared with WT kidneys, rejecting IRF-1KO kidneys showed less induction of donor MHC yet had similar mRNA levels of perforin, granzyme B, and Fas ligand and evoked host alloantibody responses. Thus in rejecting kidney transplants, IRF-1 in the graft mediates MHC induction, but it also mediates resistance to necrosis, an effect that could be crucial to permit success in interventions against rejection.
Refining Predictive Models in Critically Ill Patients with Acute Renal Failure
Authors: Mehta Ravindra L. , Pascual Maria T. , Gruta Carmencita G. , Zhuang Shunping , Chertow Glenn M. 
Published: October 2004

ABSTRACT.
Mortality rates in acute renal failure remain extremely high, and risk-adjustment tools are needed for quality improvement initiatives and design (stratification) and analysis of clinical trials. A total of 605 patients with acute renal failure in the intensive care unit during 1989-1995 were evaluated, and demographic, historical, laboratory, and physiologic variables were linked with in-hospital death rates using multivariable logistic regression. Three hundred and fourteen (51.9%) patients died in-hospital. The following variables were significantly associated with in-hospital death: age (odds ratio [OR], 1.02 per yr), male gender (OR, 2.36), respiratory (OR, 2.62), liver (OR, 3.06), and hematologic failure (OR, 3.40), creatinine (OR, 0.71 per mg/dl), blood urea nitrogen (OR, 1.02 per mg/dl), log urine output (OR, 0.64 per log ml/d), and heart rate (OR, 1.01 per beat/min). The area under the receiver operating characteristic curve was 0.83, indicating good model discrimination. The model was superior in all performance metrics to six generic and four acute renal failure-specific predictive models. A disease-specific severity of illness equation was developed using routinely available and specific clinical variables. Cross-validation of the model and additional bedside experience will be needed before it can be effectively applied across centers, particularly in the context of clinical trials.