bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in the quaternary structure of amelogenin when adsorbed onto surfaces
Authors: Tarasevich Barbara J. , Lea Scott , Bernt William , Engelhard Mark H. , Shaw Wendy J. 
Published: September 2008

AbstractAmelogenin is a unique protein that self‐assembles into spherical aggregates called “nanospheres” and is believed to be involved in controlling the formation of the highly anisotropic and ordered hydroxyapatite crystallites that form enamel. The adsorption behavior of amelogenin onto substrates is of great interest because protein‐surface interactions are critical to its function. We report studies of the adsorption of amelogenin onto self‐assembled monolayers containing COOH end group functionality as well as single crystal fluoroapatite, a biologically relevant surface. We found that although our solutions contained only nanospheres of narrow size distribution, smaller structures such as dimers or trimers were observed on the hydrophilic surfaces. This suggests that amelogenin can adsorb onto surfaces as small structures that “shed” or disassemble from the nanospheres that are present in solution. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 103–107, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Design and synthesis of backbone cyclic phosphorylated peptides: The IκB model
Authors: Qvit Nir , Hatzubai Ada , Shalev Deborah E. , Friedler Assaf , Ben‐Neriah Yinon , Gilon Chaim 
Published: September 2008

AbstractPhosphopeptides have been used to study phosphorylation and dephosphorylation, which are key events in protein expression. Backbone cyclization has been shown to increase the stability and selectivity of peptides. Backbone cyclic peptides with conformational diversity have produced bioactive peptides with improved pharmaceutical properties, metabolic stability, and enhanced intestinal permeability. We demonstrate a successful methodology for incorporating phospho‐amino acids into backbone cyclic peptides. The nuclear factor‐kappa B (NF‐κB) is a latent mammalian protein prototype of dimeric transcription factors that exists in all cell types and plays a pivotal role in a huge number of genes, such as those responsible for chronic and acute inflammatory diseases. To inhibit NF‐κB, backbone cyclic phosphopeptides were designed and synthesized based on the conserved sequence of the Inhibitor kappa B (IκB). The peptides were screened for inhibiting IκB ubiquitylation. The best compound showed 90% inhibition at a concentration of 3 μM, and its solution structure showed similarity to a related β‐catenin protein. This general methodology can be use for synthesizing cyclic phosphorylated, as well as backbone cyclic phosphorylated peptides for various biological targets. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 157–168, 2009.This article was originally published online as an accepted preprint. The “Published Online“ date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Wavelength selection using the measure of topological relevance on the self‐organizing map
Authors: Corona Francesco , Reinikainen Satu‐Pia , Aaljoki Kari , Perkiö Annikki , Liitiäinen Elia , Baratti Roberto , Simula Olli , Lendasse Amaury 
Published: September 2008

AbstractIn this work, we investigated the possibility to perform wavelength selection by exploiting the metric structure of the spectrophotoscopic measurements. The topologically preserving representation of the data is performed using the self‐organizing map (SOM) where the inputs' significance to the output is computed with the measure of topological relevance (MTR) on SOM. The MTR on SOM is a metric measuring the similarity between local distance matrices and we found that spectral inputs with a topology, which is, close to the output's are also associated to the wavelengths that chemically explain the influence of the spectra to the property of interest. As a result, we suggest a wavelength selection strategy based on the MTR on SOM, that is, interpretable to the domain experts and independent on the regression technique subsequently used for estimation. To support the presentation, a full‐scale application from the oil refining industry is illustrated on the problem of estimating standard properties in a complex hydrocarbon product starting from spectrophotoscopic measurements. The method is further validated on the problem of octane number estimation in finished gasolines, under small sample conditions. The application led to accurate, parsimonious and understandable models. Copyright © 2008 John Wiley & Sons, Ltd.
Detection and quantification of (R) and (S)‐dechloroethylifosfamide metabolites in plasma from children by enantioselective LC/MS/MS
Authors: Aleksa Katarina , Nava‐Ocampo Alejandro , Koren Gideon 
Published: September 2008

AbstractIfosfamide (IF), a potent chemotherapeutic agent for solid tumors, is known to cause high rates of nephrotoxicity in children with cancer, which is most likely due to the renal production of the metabolite chloroacetaldehyde. Using plasma samples obtained from pediatric oncology patients, we developed a simple nonderivatizing enantioselective liquid chromatography mass spectrometry method to detect the (R) and (S)‐2‐ and 3‐dechloroethylifosfamide metabolites. The (R) and (S)‐enantiomers of the 2‐ and 3‐DCEIF (N‐3‐dechlroethylifosfamide) were detectable in all 22 patients' samples with levels ranging from 9.9 to 238.7 ng/ml for (R)‐2‐DCEIF, 15.8 to 663.0 ng/ml for (S)‐2‐DCEIF, 20.8 to 852.8 ng/l for (R)‐3‐DCEIF and 28.0 to 862.0 ng/ml for (S)‐3‐DCEIF. In addition, the lower limit of quantification for this method is 1 ng/ml. Future studies should concentrate on (R) or (S) production of the 2‐DCEIF and 3‐DCEIF and subsequently chloroacetaldehyde formation with the aim of considering the administration of only the (R)‐IF as its metabolism results in a lower production of chloroacetaldehyde. Chirality, 2009. © 2008 Wiley‐Liss, Inc.
A new method for the detection of microorganisms in blood cultures: Part I. Theoretical analysis and simulation of blood culture processes
Authors: Smith Jennifer M. , Serebrennikova Yulia M. , Huffman Debra E. , Leparc German F. , García‐Rubio Luis H. 
Published: September 2008

AbstractThe physical and chemical changes occurring in blood as a consequence of microbial activity can be used as quantitative indicators of the presence of microorganisms in blood cultures. This paper reports on the theoretical analysis and computer simulation of the changes in the physical and chemical properties of blood expected as a result of the presence of microorganisms and explores the possibilities of spectrophotometric systems for the early detection of pathogens. It is concluded that multi‐wavelength reflectance methods are suitable and that the approach reported herein can lead to considerable simplifications and cost reduction of blood culture systems.
Control relevant on‐line model validation criterion based on robust stability conditions
Authors: Jiang Hailei , Shah Sirish L. , Huang Biao 
Published: September 2008

AbstractThis paper is concerned with detection and diagnosis of modelling error under closed‐loop conditions. The effect of modelling error on process output error (which is the error between the process output and the simulated output) is first analysed. Then robust stability conditions for on‐line model validation are applied. The main premise is that whenever the closed‐loop system violates the robust stability condition, it is a sign of significant process change and a signal that the control system may become potentially unstable. We relate the process output error with robust stability conditions and introduce three propositions for on‐line model validation. Any process change (or modelling error) that makes the system violate the condition specified by the robust stability theorem can be detected. Simulation examples are presented to demonstrate the applicability of the propositions. An index is also proposed to quantify modelling error in frequency domain. Simulation examples and an experimental case study are presented to demonstrate the use of the new index.
Cancer‐specific survival outcomes among patients treated during the cytokine era of kidney cancer (1989‐2005)
Authors: Belldegrun Arie S. , Klatte Tobias , Shuch Brian , LaRochelle Jeffrey C. , Miller David C. , Said Jonathan W. , Riggs Stephen B. , Zomorodian Nazy , Kabbinavar Fairooz F. , deKernion Jean B. , Pantuck Allan J. 
Published: September 2008

AbstractBACKGROUND.The management of renal cell carcinoma (RCC) is evolving toward less extirpative surgery and the use of targeted therapy. The authors set out to provide a benchmark against which emerging therapies should be measured.METHODS.A prospective database including clinical and pathological variables for 1632 patients with RCC treated between 1989 and 2005 was queried. Patients were stratified using the University of California‐Los Angeles Integrated Staging System (UISS) into low‐, intermediate‐, and high‐risk groups. Disease‐specific survival (DSS) was measured. Response to systemic therapy for patients with advanced disease was assessed.RESULTS.Nephrectomy was performed in 1492 patients. Overall 5‐, 10‐, and 15‐year DSS was 55%, 40%, and 29%. For localized disease, 5‐ and 10‐year DSS for UISS low‐, intermediate‐, and high‐risk groups was 97% and 92%, 81% and 61%, and 62% and 41%, respectively. For metastatic disease, 5‐ and 10‐year DSS for UISS low‐, intermediate‐, and high‐risk groups was 41% and 31%, 18% and 7%, and 8% and 0%, respectively. Patients with metastatic disease receiving immunotherapy (n = 453) had complete response in 7% (median survival [MS], 120+ months), partial response in 15% (MS, 42.8 months), stable disease in 33% (MS, 38.6 months), and progressive disease in 45% (MS, 11.6 months).CONCLUSIONS.Most patients with localized RCC do well with surgery alone, but effective adjuvant therapy is needed for patients identified as at high risk for recurrence. For advanced disease, newer targeted and potentially less toxic treatments should be at least as effective as those achieved with aggressive surgical resection and immunotherapy. Cancer 2008. © 2008 American Cancer Society.
Short‐term effects of treatment‐induced hormonal changes on cognitive function in breast cancer patients
Authors: Hermelink Kerstin , Henschel Volkmar , Untch Michael , Bauerfeind Ingo , Lux Michael Patrick , Munzel Karin 
Published: September 2008

AbstractBACKGROUND.It is suspected that estrogen depletion resulting from treatment may contribute to cognitive compromise in patients with breast cancer. However, the evidence for estrogen effects on cognition is inconclusive, and the consequences of hormonal changes for cognitive function in patients with cancer rarely have been investigated. In this study, the authors investigated the effects of treatment‐induced menopause and antiestrogen therapy with tamoxifen and aromatase inhibitors (AIs) on cognitive function.METHODS.Cognitive performance was assessed in 101 patients with breast cancer before the start of cancer therapy (T1), toward the end of neoadjuvant chemotherapy (T2), and 1 year after baseline (T3) using 12 cognitive tests. Menopause occurred in a subgroup of patients, and an overlapping subgroup started antiestrogen therapy with tamoxifen or AIs. Linear mixed‐effects models that made it possible to determine effects at group levels and individual levels simultaneously were used for statistical analysis.RESULTS.At the group level, a significant favorable effect of induced menopause emerged in a test of executive function (P = .0035). Two additional group‐level effects of induced menopause, both favorable, and 2 individual‐level effects that were positive in some patients and negative in others were not significant when multiple testing was taken into account. No significant effects of tamoxifen or AIs on cognitive function were observed.CONCLUSIONS.Hormonal changes did not appear to contribute to cognitive compromise in patients with breast cancer during the first year after diagnosis. Antiestrogen treatment with tamoxifen or AIs did not affect cognition, and the effects of induced menopause were more likely to be favorable. However, the possibility that some cognitive decline occurs in individual patients could not be excluded. Cancer 2008. © 2008 American Cancer Society.
Genetic variations in cell‐cycle pathway and the risk of oral premalignant lesions
Authors: Ye Yuanqing , Lippman Scott M. , Lee J. Jack , Chen Meng , Frazier Marsha L. , Spitz Margaret R. , Wu Xifeng 
Published: September 2008

AbstractBACKGROUND.Cell‐cycle checkpoint controls regulate cell‐cycle progression and proliferation. Alterations in cell‐cycle control mechanisms are linked to tumorigenesis.METHODS.This case‐control study included 147 cases and 147 controls. The authors used a pathway‐based approach to assess the association between 10 potential functional single‐nucleotide polymorphisms from 7 cell‐cycle control genes and the risk of oral premalignant lesions (OPLs). They also used classification and regression tree analysis to examine high‐order gene‐gene and gene‐smoking interactions.RESULTS.Compared with the homozygous wild‐type GG genotype of CCND1 P241P, individuals with the AG genotype exhibited an increased risk of OPL (odds ratio, 1.58; 95% confidence interval, 0.89‐2.83), and carriers of the AA genotype had a significantly increased risk of OPL (odds ratio, 2.75; 95% confidence interval, 1.33‐5.71), with risk increasing significantly with the increasing number of variant alleles (P = .006). The risk of OPL increased significantly as the number of unfavorable genotypes in the pathway increased (P = .002). The final decision tree in the classification and regression tree analysis contained 5 terminal nodes. Compared with the never smokers (the lowest risk group), the odds ratios for terminal nodes 2 through 5 ranged from 1.21 to 5.40.CONCLUSIONS.The results illustrated the advantage of using a pathway‐based approach for analyzing gene‐gene and gene‐smoking interactions. Specifically, the authors showed that genetic polymorphisms in cell‐cycle control pathway genes may contribute to the risk of OPL. Cancer 2008. © 2008 American Cancer Society.
Risk of radiation‐related salivary gland carcinomas among survivors of Hodgkin lymphoma
Authors: Boukheris Houda , Ron Elaine , Dores Graça M. , Stovall Marilyn , Smith Susan A. , Curtis Rochelle E. 
Published: September 2008

AbstractBACKGROUND.Radiotherapy for Hodgkin lymphoma (HL) increases the risk of salivary gland carcinomas (SGC). To the authors' knowledge, however, the magnitude of the risk has not been assessed to date.METHODS.The risks of SGC among 20,928 1‐year survivors of HL who were diagnosed between 1973 and 2003 were evaluated in 11 population‐based cancer registry areas of the Surveillance, Epidemiology, and End Results (SEER) program. Observed‐to‐expected ratios (O/E) were assessed by radiation treatment, sex, age at the time of HL diagnosis, calendar year of diagnosis, attained age, time since HL diagnosis, histologic type of SGC, and site of occurrence in the major salivary glands.RESULTS.Among 11,047 HL patients who received radiotherapy as part of their initial treatment for HL, 21 developed subsequent invasive SGC (O/E = 16.9; 95% confidence interval [95% CI], 10.4‐25.8). The risk of radiation‐related SGC was highest for younger HL patients (age <20 years) (O/E = 45.5; 95% CI, 12.4‐116.5) and among 10‐year survivors (O/E = 23.9; 95% CI, 13.1‐40.1), with risks remaining elevated for at least 2 decades after irradiation. Significant differences in risk by histologic type were observed, with a particularly high risk of developing mucoepidermoid carcinomas (O = 14; O/E = 44.2 [95% CI, 24.2‐74.2]) and adenocarcinomas (O = 4; O/E = 30.6 [95% CI, 8.3‐78.2]) noted.CONCLUSIONS.HL patients treated with radiotherapy experienced a significantly increased risk of SGC, particularly when exposed at young ages or for at least 2 decades after exposure. Although the results of the current study reflect the late effects of former HL treatment approaches, they point to the importance of long‐term follow‐up and a heightened awareness of SGC risk in this population. Cancer 2008. Published 2008 by the American Cancer Society.
CD4 and CD8 enumeration for HIV monitoring in resource‐constrained settings
Authors: Li Xiao , Breukers Christian , Ymeti Aurel , Lunter Björn , Terstappen Leon W. M. M. , Greve Jan 
Published: September 2008

AbstractBackground:We developed a volumetric single platform image cytometer (SP ICM) that is dedicated to count CD4+ and CD8+ T lymphocytes for HIV monitoring in resource‐constrained settings. The instrument was designed to be low‐cost, yet reliable, easy‐to‐use, and robust.Methods:Whole blood is incubated with CD3‐magnetic nanoparticles, CD4‐phycoerythrin (PE), and CD8‐peridinin‐chlorophyll‐protein complex (PerCP). The CD3 cells are immunomagnetically attracted to an analysis surface, where fluorescence images of CD4+ and CD8+ T lymphocytes are recorded and analyzed, respectively. We compared CD4, CD8 counts, and CD4/CD8 ratio obtained by the SP ICM with those from a SP flow cytometer (FCM) tetraCXP method on blood samples from 145 patients.Results:Good correlations were obtained (R: 0.96–0.99) between the SP ICM and the SP FCM. There was ∼10% CD8 undercount in the SP ICM, which could be partly caused by CD8+dim T lymphocytes that were not detected by the instrument or not counted by the image analysis due to the cross‐talk from the CD4‐PE signal in the CD8‐PerCP image.Conclusions:The SP ICM is a good candidate for HIV monitoring in point‐of‐care settings of resource‐constrained countries. © 2008 Clinical Cytometry Society
A comparison of multiplex suspension array large‐panel kits for profiling cytokines and chemokines in rheumatoid arthritis patients
Authors: Khan Imran H. , Krishnan V. V. , Ziman Melanie , Janatpour Kim , Wun Ted , Luciw Paul A. , Tuscano Joseph 
Published: September 2008

AbstractBackgroundMultiplex analysis allows measurements of a large number of analytes simultaneously in each sample. On the basis of the Luminex multiplex technology (xMAP), kits for measuring multiple cytokines and chemokines (immunomodulators) are commercially available and are useful in investigations on inflammatory diseases. This study evaluated four multiplex kits (Bio‐Plex, LINCOplex, Fluorokine, and Beadlyte) that contained 27, 29, 20, and 22 analytes each, respectively, for the analysis of immunomodulators in plasma of patients with rheumatoid arthritis (RA) who underwent treatment with antibody against CD20 (rituximab), a B‐cell reductive therapy.MethodsMultiplex kits were tested on serial plasma samples obtained from six RA patients at baseline and multiple time points (3, 6, and 9 months) post‐treatment with rituximab. The RA patients included in this study had previously failed therapy with disease modifying anti‐arthritis drugs (DMARD) and treatment with anti‐TNFα antibody (infliximab).ResultsComputer modeling and hierarchical cluster analysis of the multiplex data allowed a comparison of the performance of multiplex assay kits and revealed profiles of immunomodulators in the RA patients.ConclusionsIn plasma of RA patients who appeared to have benefited from the rituximab treatment, the profile of significantly elevated immunomodulators by at least two of the three kits (BioPlex, LINCOplex, Beadlyte) is as follows: IL‐12p70, Eotaxin, IL‐4, TNFα, Il‐9, IL‐1β, IFNγ, IL‐10, IL‐6, and IL‐13. Immunomodulator profiling by multiplex analysis may provide useful plasma biomarkers for monitoring response to B‐cell reductive therapy in RA patients. © 2008 Clinical Cytometry Society
A rapid, fluorescence‐based assay for detecting antigenic modulation of the acetylcholine receptor on human cell lines
Authors: Keefe Dennis , Hess Donna , Bosco Jennifer , Tzartos Socrates , Powell Jan , Lamsa Justin , Josiah Serene 
Published: September 2008

AbstractBackground:Myasthenia gravis (MG) is an autoimmune disease affecting ∼40,000 patients in the United States. One of the major mechanisms of disease pathology in MG is the binding, internalization, and eventual destruction of acetylcholine receptors (AChR) at the neuromuscular junction by cross‐linking AChR‐specific autoantibodies. This process, known as antigenic modulation, ultimately attenuates the ability of muscle cells to contract in response to signals from neurons, leading to muscle weakness and fatigue. For this reason, antigenic modulation of the AChR on cultured cells has become an important diagnostic tool for assessing the pathogenicity of AChR‐specific autoantibodies. Traditionally, these assays have been done using radiolabeled AChR ligands such as 125I alpha‐bungarotoxin to determine relative AChR number. Here, we present a high‐throughput immunofluorescent flow cytometry‐based assay that can be used to quantify AChR levels on the cell surface and assess the efficacy of molecules designed to rescue antigenic modulation.Methods:AChR levels were quantified on human muscle cells before and after treatment with AChR antibodies via immunofluorescent labeling with the AChR monoclonal antibodies, mAb210 and mAb B3, followed by flow cytometry of EDTA‐treated cells.Results:Using a novel, flow cytometry‐based assay, antigenic modulation of the AChR was demonstrated on human cells using both AChR‐specific monoclonal antibody and MG patient serum. The degree of antigenic modulation was dose responsive to antibody levels and could be reversed by preincubating antibodies with soluble AChR alpha subunit extracellular domain.Summary:A rapid, nonradioactive assay was developed to determine the potential of AChR‐specific antibodies in the serum of MG patients to bind and down‐regulate the AChR. This assay can be used to assess the ability of putative therapeutics that rescue antigenic modulation and could be developed for the treatment of MG. © 2008 Clinical Cytometry Society
PD‐1 ligands expressed on myeloid‐derived APC in the CNS regulate T‐cell responses in EAE
Authors: Schreiner Bettina , Bailey Samantha L. , Shin Tahiro , Chen Lieping , Miller Stephen D. 
Published: September 2008

AbstractDisease progression in experimental autoimmune encephalomyelitis (EAE) is regulated by programmed death receptor 1 (PD‐1) and its ligands, B7‐H1 (programmed death ligand 1 (PD‐L1)) and B7‐DC (PD‐L2). B7‐H1 and B7‐DC have negative regulatory effects upon binding PD‐1 on activated T cells and B7‐H1 deficiency increases severity of both diabetes and EAE. However, the role of PD‐L expression on different APC in the CNS in regulating local T‐cell function during relapsing EAE has not been examined. Our data show that the majority of CNS CD4+ T cells isolated during acute EAE are PD‐1+, and T cells specific for relapse‐associated epitopes express PD‐1 upon antigen stimulation in the CNS. B7‐H1 and B7‐DC are differentially expressed on discrete APC populations in the inflamed CNS. B7‐H1 and PD‐1 have mainly inhibitory functions on CNS T cells. B7‐H1 negatively regulates the stimulation of activated PD‐1+ TH cells, in co‐cultures with microglia and different CNS‐infiltrating APC presenting endogenously processed peptides. The preponderance of IFN‐γ+ versus IL‐17+ T cells in the CNS of B7‐H1−/− mice suggests that B7‐H1 more selectively suppresses TH‐1 than TH‐17 responses in vivo. In contrast, blockade of B7‐DC has less pronounced regulatory effects. Overall, the results demonstrate that B7‐H1 expressed by CNS myeloid APC negatively regulates T‐cell activation during acute relapsing EAE.