bluuebunny/crossref_metadata_2025 huggingface dataset:
Survival Prediction in Patients With Glioblastoma Multiforme by Human Telomerase Genetic Variation
Authors: Wang Luo , Wei Qingyi , Wang Li-E , Aldape Kenneth D. , Cao Yumei , Okcu M. Fatih , Hess Kenneth R. , El-Zein Randa , Gilbert Mark R. , Woo Shiao Y. , Prabhu Sujit S. , Fuller Greg N. , Bondy Melissa L.
Published: March 2006

Purpose

Glioblastoma multiforme (GBM) is the most common and aggressive glioma with the poorest survival. Use of biomarkers for screening patients with GBM may be used to modify treatments and improve outcomes. The level of human telomerase (hTERT) expression is an independent predictor of outcome of many cancers, and a functional variant of hTERT MNS16A (shorter tandem repeats or short [S] allele) is associated with increased hTERT mRNA expression. We investigated whether hTERT MNS16A variant genotype predicted survival in GBM patients.

Patients and Methods

We genotyped hTERT MNS16A in 299 GBM patients using polymerase chain reaction and determined hTERT genotype by classifying the DNA band of 243 or 272 base pairs (bp) as S allele and 302 or 333 bp as long (L) allele. We compared overall survival using Kaplan-Meier estimates and equality of survival distributions using the log-rank test, and we computed univariate and multivariate Cox proportional hazards models to estimate the effects of selected variables.

Results

Overall survival differed significantly by hTERT MNS16A genotype, with median survivals of 25.1, 14.7, and 14.6 months for the SS, SL, and LL genotypes, respectively. Compared with the SS genotype, the hazard ratios for the SL and LL genotypes were 1.69 and 1.87, respectively, after adjustment for other factors. Multivariate Cox regression analysis showed an independent statistically significant association between the hTERT MNS16A variant genotype and outcome.

Conclusion

A functional hTERT MNS16A genotype is a potential biomarker for assessment of survival outcome of GBM. Larger studies are needed to verify these findings.
Human Telomere Reverse Transcriptase Expression Predicts Progression and Survival in Pediatric Intracranial Ependymoma
Authors: Tabori Uri , Ma Jing , Carter Michael , Zielenska Maria , Rutka James , Bouffet Eric , Bartels Ute , Malkin David , Hawkins Cynthia
Published: March 2006

Purpose

Pediatric intracranial ependymomas are a heterogeneous group of neoplasms with unpredictable clinical and biologic behavior. As part of ongoing studies to identify potential biologic and therapeutic markers, we analyzed the role of human telomere reverse transcriptase (hTERT; the catalytic subunit of telomerase) expression as a prognostic marker for this disease.

Patients and Methods

Primary intracranial ependymomas that were resected at our institution between 1986 and 2004 were identified through the pathology and oncology databases. A tissue array was constructed from the patient samples and hTERT expression was evaluated by immunohistochemistry. Twenty-one samples were also analyzed for telomerase activity (telomerase repeat amplification protocol assay).

Results

Eighty-seven tumors from 65 patients were analyzed. Five-year progression-free survival was 57% (SEM, 12%) and 21% (SEM, 8%) for hTERT-negative and hTERT-positive tumors, respectively (P = .002). Five-year overall survival was 84% (SEM, 7%) and 41% (SEM, 7%) for hTERT-negative and hTERT-positive tumors, respectively (P = .001). There was good correlation between telomerase activity and hTERT expression (κ = 0.637). Multivariate analysis revealed hTERT expression to be the single most important predictor of survival of all known pathologic, clinical, and treatment factors (hazard ratio, 60.4; 95% CI, 6.4 to 561). All four patients with hTERT-negative tumors at relapse are still alive, with median follow-up of 11.2 years.

Conclusion

In this study, hTERT expression was the strongest predictor of outcome and was independent of other clinical and pathologic prognostic markers. It represents a simple and reliable biologic prognostic factor for intracranial ependymomas. These results should be confirmed in larger prospective trials.
Skip Metastases in Osteosarcoma: Experience of the Cooperative Osteosarcoma Study Group
Authors: Kager Leo , Zoubek Andreas , Kastner Ulrike , Kempf-Bielack Beate , Potratz Jenny , Kotz Rainer , Exner G. Ulrich , Franzius Christiane , Lang Susanna , Maas Rainer , Jürgens Heribert , Gadner Helmut , Bielack Stefan
Published: March 2006

Purpose

The outlook for patients with osteosarcoma who present with synchronous regional bone metastases (skip metastases), either in the primary bone site or transarticular, is considered to be extremely poor. This study was conducted to further investigate the prognostic implication of skip metastases in osteosarcoma.

Patients and Methods

The authors retrospectively analyzed the collected data of 1,765 consecutive patients with newly diagnosed high-grade osteosarcoma of bone who were registered in the neoadjuvant Cooperative Osteosarcoma Study Group studies and identified 24 patients (1.4%) with unequivocally proven skip metastases. All 24 patients were treated by an aggressive surgical approach coupled with polychemotherapy. Demographic, diagnostic, tumor, and treatment-related variables and response and survival data were analyzed.

Results

Skip metastases were identified preoperatively in 11 of 24 patients by bone scan, eight of 22 patients by plain x-ray, 15 of 18 patients by magnetic resonance imaging, and five of 10 patients by computed tomography. A complete surgical remission (CSR) of all clinically detectable tumor sites was achieved in 22 of 24 patients during front-line therapy. With a median follow-up time of 4.4 years (8 years for survivors) from diagnosis, 12 patients were alive, all of whom were in continuous CSR. Survival did correlate with location of skip metastases and histologic response to neoadjuvant chemotherapy.

Conclusion

Synchronous regional bone metastases are rare in osteosarcoma, and preoperative detection relies on appropriate diagnostic imaging. Aggressive multimodal therapy holds the promise to achieve prolonged survival, especially in patients in whom these metastases occur within the same bone as the primary lesion and whose tumors respond well to chemotherapy.
Translocation Carcinomas of the Kidney After Chemotherapy in Childhood
Authors: Argani Pedram , Laé Marick , Ballard Edgar T. , Amin Mahul , Manivel Carlos , Hutchinson Brian , Reuter Victor E. , Ladanyi Marc
Published: March 2006

Purpose

Children who survive cancer are at more than 19-fold increased risk of developing another malignancy. Renal cell carcinoma (RCC) occurring as a secondary malignancy is uncommon. Translocation RCC, bearing TFE3 or TFEB gene fusions, are recently recognized entities for which risk factors have not been identified.

Patients and Methods

We describe the clinical, pathologic, cytogenetic, and molecular data on six translocation RCCs that arose in five young patients who had received chemotherapy.

Results

The ages at time of diagnosis of the RCC ranged from 6 to 22 years. Histologically, these tumors showed typical features previously described for translocation RCCs. At the molecular level, three tumors contained the ASPL-TFE3 fusion, two contained Alpha-TFEB, and one contained PRCC-TFE3. The intervals between chemotherapy and the diagnosis of RCC ranged from 4 to 13 years. The indications for the antecedent chemotherapy were varied and included acute promyelocytic leukemia, acute myeloid leukemia with t(9;11), bilateral Wilms' tumor, systemic lupus erythematosus, and conditioning regimen of bone marrow transplant for Hurler's syndrome. Only the latter patient had also received radiation. Hence, among 39 genetically confirmed translocation RCCs in our personal experience, six (15%) have arisen in patients who had received cytotoxic chemotherapy.

Conclusion

Cytotoxic chemotherapy may predispose to the development of renal translocation carcinomas.
Randomized Trial of Peer Counseling on Reproductive Health in African American Breast Cancer Survivors
Authors: Schover Leslie R. , Jenkins Rosell , Sui Dawen , Adams Jennifer Harned , Marion Michelle S. , Jackson Karen Eubanks
Published: March 2006

Purpose

We designed a peer counseling program to improve sexual function, increase knowledge about reproductive health, and decrease menopausal symptoms and infertility-related distress for African American breast cancer survivors.

Patients and Methods

Women were randomly assigned to immediate counseling or a 3-month waitlist. Three peer counselors conducted a 3-session intervention using a detailed workbook. Questionnaires at baseline, after the waitlist period, at posttreatment, and at 3-month follow-up assessed spirituality, sexual function, menopause symptoms, emotional distress, relationship satisfaction, fertility concerns, and knowledge about reproductive health and breast cancer. At the postcounseling assessment, women rated the workbook, their counselor, and the program.

Results

Of 93 women screened, 60 women (65%) enrolled in the study. Women who completed counseling (80%; N = 48) had a mean age of 49 years (standard deviation [SD], 8 years) and a mean follow-up of 4.5 years (SD, 3.8 years) since cancer diagnosis. Almost all rated the workbook as very easy to understand (94%) and their counselor as very knowledgeable (96%) and very skillful (98%). Eighty-one percent rated the program as “very useful to me.” Immediate counseling and waitlist groups did not differ at baseline in psychologic adjustment, nor did scores change during the waitlist period. Therefore, the groups were combined in analyzing outcomes. Knowledge of reproductive issues improved significantly from baseline to 3-month follow-up (P < .0001), as did emotional distress (P = .0047) and menopause symptoms (P = .0128). Sexually dysfunctional women became less distressed (P = .0167).

Conclusion

Women valued the Sisters Peer Intervention in Reproductive Issues After Treatment program highly and found it relevant. The program had positive effects on knowledge and target symptoms.
Role of Radiotherapy in Supratentorial Primitive Neuroectodermal Tumor in Young Children: Results of the German HIT-SKK87 and HIT-SKK92 Trials
Authors: Timmermann Beate , Kortmann Rolf-Dieter , Kühl Joachim , Rutkowski Stefan , Meisner Christof , Pietsch Torsten , Deinlein Frank , Urban Christian , Warmuth-Metz Monika , Bamberg Michael
Published: March 2006

Purpose

To assess the outcome of young children with supratentorial primitive neuroectodermal tumor (stPNET) treated by intensive postoperative chemotherapy alone compared with treatment with chemotherapy and delayed radiotherapy (RT).

Patients and Methods

From 1987 to 1992, children younger than 3 years of age with stPNET were enrolled in the HIT-SKK87 trial in Germany and Austria. After surgery, low-risk patients received maintenance chemotherapy before RT. In high-risk patients, intensive induction chemotherapy was followed by maintenance chemotherapy until delayed RT was initiated. In the following trial, HIT-SKK92 methotrexate-based chemotherapy was applied. In children with complete remission after three cycles, therapy was finished without irradiation. Otherwise, radiotherapy or salvage chemotherapy was administered.

Results

Twenty-nine children were eligible (age, 3.0 to 37.0 months). All children received chemotherapy. In 15 children, no RT was administered. Four children had tumor progression during chemotherapy and underwent irradiation. In 10 patients, RT was given after chemotherapy. Overall survival (OS) and progression-free survival (PFS) rates after 3 years were 17.2% and 14.9%, respectively. Twenty-four children relapsed (13 at the tumor site only, three at distant site, and eight at both local and distant sites). Positive impact on survival was observed in children with complete resection but without statistical significance. Administration of RT was the only significant predictive factor for OS and PFS. Only one child not having RT survived.

Conclusion

Outcome of infants and babies with stPNET is unsatisfactory. Omission of RT jeopardizes survival, even if intensive chemotherapy is applied. We suggest to limit any delay of RT to a maximum of 6 months even in young children.
White Race As a Risk Factor for Hypothyroidism After Treatment for Pediatric Hodgkin's Lymphoma
Authors: Metzger Monika L. , Hudson Melissa M. , Somes Grant W. , Shorr Ron I. , Li Chin-Shang , Krasin Matthew J. , Shelso John , Pui Ching-Hon , Howard Scott C.
Published: March 2006

Purpose

Hypothyroidism frequently occurs after treatment for pediatric Hodgkin's lymphoma, but race has not been investigated as a risk factor for this delayed toxicity. The aim of this study was to determine whether race is an independent risk factor for hypothyroidism in survivors of pediatric Hodgkin's lymphoma.

Patients and Methods

To identify differences between black and white patients in the development of hypothyroidism after treatment for Hodgkin's lymphoma, we conducted a retrospective study of consecutively treated pediatric patients with newly diagnosed Hodgkin's lymphoma treated at St Jude Children's Research Hospital (Memphis, TN) from January 1980 through December 2002. Clinical or biochemical hypothyroidism was defined by an above normal thyroxine-stimulating hormone concentration or by the need for thyroid hormone replacement therapy.

Results

The 461 patients (388 white patients, 73 black patients) where followed for a median of 11.3 years (range, 1.8 to 24.9 years). Hypothyroidism developed in 196 (43%) of 461 patients after a median of 2.9 years (range, 0.7 to 11.3 years) after diagnosis of Hodgkin's lymphoma. Hypothyroidism developed in 47% of white patients but in only 21% of black patients (hazard ratio = 2.7; 95% CI, 1.6 to 4.6). After adjusting for other risk factors for hypothyroidism (thyroid radiation dose, sex, and nodular sclerosis histology), the risk of hypothyroidism in white patients was 2.5 times (95% CI, 1.5 to 4.3 times) the risk in black patients (P < .001).

Conclusion

White patients have a higher risk of hypothyroidism after neck irradiation for pediatric Hodgkin's lymphoma than black patients.
Neuropeptide S Stimulates the Hypothalamo-Pituitary-Adrenal Axis and Inhibits Food Intake
Authors: Smith Kirsty L. , Patterson Michael , Dhillo Waljit S. , Patel Sejal R. , Semjonous Nina M. , Gardiner James V. , Ghatei Mohammad A. , Bloom Stephen R.
Published: March 2006

Neuropeptide S (NPS) is a recently discovered peptide shown to be involved in the modulation of arousal and fear responses. It has also been shown that lateral ventricle administration of NPS causes a significant decrease in food intake. Neuropeptides involved in the modulation of arousal have been shown to be involved in the regulation of the hypothalamo-pituitary adrenal (HPA) axis and food intake. In this study, we have examined the effect of intracerebroventricular (ICV) administration of NPS on behavior, regulation of the HPA axis, and food intake. ICV NPS significantly increased plasma ACTH and corticosterone 10 and 40 min after injection, respectively. A single ICV injection of NPS caused a significant increase in rearing activity as well as ambulatory movement for up to 45 min after injection. We then studied the effect of paraventricular nucleus (PVN) administration of NPS on the regulation of the HPA axis, behavior, and food intake. There was a significant increase in plasma ACTH and corticosterone after a single NPS PVN injection. Incubation of hypothalamic explants with increasing concentrations of NPS caused a significant increase in CRH and arginine vasopressin release. In addition, PVN administration of NPS dose-dependently inhibited food intake in the first hour after injection, although no effect on food intake was seen after this time. PVN administration of NPS caused a significant increase in rearing activity. These data demonstrate a novel role for NPS in the stimulation of the HPA axis.
Seminal Plasma Promotes the Expression of Tumorigenic and Angiogenic Genes in Cervical Adenocarcinoma Cells via the E-Series Prostanoid 4 Receptor
Authors: Muller Melissa , Sales Kurt J. , Katz Arieh A. , Jabbour Henry N.
Published: March 2006

E-series prostanoid (EP)4 receptor is up-regulated in numerous cancers, including cervical carcinomas, and has been implicated in mediating the effects of prostaglandin (PG)E2 in tumorigenesis. In addition to regulation by endogenously biosynthesized PGE2, neoplastic cervical epithelial cells in sexually active women may also be regulated by PGs present in seminal plasma. In this study, we investigated the signal transduction pathways mediating the role of seminal plasma and PGE2 in the regulation of tumorigenic and angiogenic genes via the EP4 receptor in cervical adenocarcinoma (HeLa) cells. HeLa cells were stably transfected with EP4 receptor in the sense orientation. Seminal plasma and PGE2 signaling via the EP4 receptor induced the activation of cyclooxygenase (COX)-2 and vascular endothelial growth factor (VEGF) promoters, expression of COX-2 and VEGF mRNA and protein, and secretion of VEGF protein into the culture medium. Treatment of HeLa cells with seminal plasma or PGE2 also rapidly induced the phosphorylation of ERK1/2 via the EP4 receptor. Preincubation of cells with a specific EP4 receptor antagonist (ONO-AE2-227) or chemical inhibitors of epidermal growth factor receptor (EGFR) tyrosine kinase or MAPK kinase or cotransfection of cells with dominant-negative mutant cDNA targeted against the EGFR, serine/threonine kinase Raf, or MAPK kinase abolished the EP4-induced activation of COX-2, VEGF, and ERK1/2. Therefore, we have demonstrated that seminal plasma and PGE2 can promote the expression of tumorigenic and angiogenic factors, in cervical adenocarcinoma cells via the EP4 receptor, EGFR, and ERK1/2 signaling pathways.
Activation of the Hypothalamo-Pituitary-Adrenal Axis by Isolation and Restraint Stress during Lactation in Ewes: Effect of the Presence of the Lamb and Suckling
Authors: Tilbrook A. J. , Turner A. I. , Ibbott M. D. , Clarke I. J.
Published: March 2006

We investigated the effect of the presence and absence of lambs and suckling by lambs to attenuate activation of the hypothalamo-pituitary-adrenal (HPA) axis to isolation and restraint stress in lactating sheep. In experiment 1, blood samples were collected every 10 min from nonlactating (n = 5) and lactating (n = 5) ewes for 4 h before and during stress. In experiment 2, ewes (n = 6) were allocated to 1) nonlactating, 2) lactating with lambs absent, 3) lactating with lambs present but unable to suckle, and 4) lactating with lambs present and able to suckle. Blood samples were collected over 8 h with no stress (control day) and for 4 h before and 4 h during stress (stress day). In experiment 1, the mean (±sem) cortisol concentrations increased significantly (P < 0.05) in nonlactating ewes during stress but did not change in lactating ewes. In experiment 2, cortisol did not vary on the control day or pretreatment of the stress day but increased (P < 0.05) during stress in all groups except lactating ewes with lambs present and able to suckle. The greatest cortisol response occurred in nonlactating ewes followed by lactating ewes with lambs absent and lactating ewes with lambs present but unable to suckle. During stress, the ACTH concentrations increased (P < 0.05) in nonlactating ewes and lactating ewes with lambs absent but not in lactating ewes with lambs present. We conclude that the activity of the HPA axis during isolation and restraint is reduced in lactating ewes and that the presence of lambs increases this level of attenuation.
Vascular Endothelial Growth Factor Receptor-2 Expression Is Induced by 17β-Estradiol in ZR-75 Breast Cancer Cells by Estrogen Receptor α/Sp Proteins
Authors: Higgins Kelly J. , Liu Shengxi , Abdelrahim Maen , Yoon Kyungsil , Vanderlaag Kathryn , Porter Weston , Metz Richard P. , Safe Stephen
Published: March 2006

Vascular endothelial growth factor receptor-2 kinase insert domain receptor (VEGFR2/KDR) is critical for angiogenesis, and VEGFR2 mRNA and protein are expressed in ZR-75 breast cancer cells and induced by 17β-estradiol (E2). Deletion analysis of the VEGFR2 promoter indicates that the proximal GC-rich region is required for both basal and hormone-induced transactivation, and mutation of one or both of the GC-rich motifs at −58 and −44 results in loss of transactivation. Electrophoretic mobility shift and chromatin immunoprecipitation assays show that Sp1, Sp3, and Sp4 proteins bind the GC-rich region of the VEGFR2 promoter. Results of the chromatin immunoprecipitation assay also demonstrate that ERα is constitutively bound to the VEGFR2 promoter and that these interactions are not enhanced after treatment with E2, whereas ERα binding to the region of the pS2 promoter containing an estrogen-responsive element is enhanced by E2. RNA interference studies show that hormone-induced activation of the VEGFR2 promoter constructs requires Sp3 and Sp4 but not Sp1, demonstrating that hormonal activation of VEGFR2 involves a nonclassical mechanism in which ERα/Sp3 and ERα/Sp4 complexes activate GC-rich sites where Sp proteins but not ERα bind DNA. These results show for the first time that Sp3 and Sp4 cooperatively interact with ERα to activate VEGFR2 and are in contrast to previous results showing that several hormone-responsive genes are activated by ERα/Sp1 in breast cancer cell lines.
Linking Ligand-Induced Alterations in Androgen Receptor Structure to Differential Gene Expression: A First Step in the Rational Design of Selective Androgen Receptor Modulators
Authors: Kazmin Dmitri , Prytkova Tatiana , Cook C. Edgar , Wolfinger Russell , Chu Tzu-Ming , Beratan David , Norris J. D. , Chang Ching-yi , McDonnell Donald P.
Published: March 2006

We have previously identified a family of novel androgen receptor (AR) ligands that, upon binding, enable AR to adopt structures distinct from that observed in the presence of canonical agonists. In this report, we describe the use of these compounds to establish a relationship between AR structure and biological activity with a view to defining a rational approach with which to identify useful selective AR modulators. To this end, we used combinatorial peptide phage display coupled with molecular dynamic structure analysis to identify the surfaces on AR that are exposed specifically in the presence of selected AR ligands. Subsequently, we used a DNA microarray analysis to demonstrate that differently conformed receptors facilitate distinct patterns of gene expression in LNCaP cells. Interestingly, we observed a complete overlap in the identity of genes expressed after treatment with mechanistically distinct AR ligands. However, it was differences in the kinetics of gene regulation that distinguished these compounds. Follow-up studies, in cell-based assays of AR action, confirmed the importance of these alterations in gene expression. Together, these studies demonstrate an important link between AR structure, gene expression, and biological outcome. This relationship provides a firm underpinning for mechanism-based screens aimed at identifying SARMs with useful clinical profiles.
Activation of the Blue Opsin Gene in Cone Photoreceptor Development by Retinoid-Related Orphan Receptor β
Authors: Srinivas Maya , Ng Lily , Liu Hong , Jia Li , Forrest Douglas
Published: March 2006

Color vision requires the expression of opsin photopigments with different wavelength sensitivities in retinal cone photoreceptors. The basic color visual system of mammals is dichromatic, involving differential expression in the cone population of two opsins with sensitivity to short (S, blue) or medium (M, green) wavelengths. However, little is known of the factors that directly activate these opsin genes and thereby contribute to the S or M opsin identity of the cone. We report that the orphan nuclear receptor RORβ (retinoid-related orphan receptor β) activates the S opsin gene (Opn1sw) through binding sites upstream of the gene. RORβ lacks a known physiological ligand and activates the Opn1sw promoter modestly alone but strongly in synergy with the retinal cone-rod homeobox factor (CRX), suggesting a cooperative means of enhancing RORβ activity. Comparison of wild-type and mutant lacZ reporter transgenes showed that the RORβ-binding sites in Opn1sw are required for expression in mouse retina. RORβ-deficient mice fail to induce S opsin appropriately during postnatal cone development. Photoreceptors in these mice also lack outer segments, indicating additional functions for RORβ in photoreceptor morphological maturation. The results identify Opn1sw as a target gene for RORβ and suggest a key role for RORβ in regulating opsin expression in the color visual system.
Recognition of RNA by the p53 tumor suppressor protein in the yeast three-hybrid system
Authors: RILEY KASANDRA J.-L. , CASSIDAY LAURA A. , KUMAR AKASH , MAHER L. JAMES
Published: March 2006

The p53 tumor suppressor protein is a homotetrameric transcription factor whose gene is mutated in nearly half of all human cancers. In an unrelated screen of RNA/protein interactions using the yeast three-hybrid system, we inadvertently detected p53 interactions with several different RNAs. A literature review revealed previous reports of both sequence-specific and -non-specific interactions between p53 and RNA. Using yeast three-hybrid selections to identify preferred RNA partners for p53, we failed to identify primary RNA sequences or obvious secondary structures required for p53 binding. The cationic p53 C-terminus was shown to be required for RNA binding in yeast. We show that while p53 strongly discriminates between certain RNAs in the yeast three-hybrid assay, the same RNAs are bound equally by p53 in vitro. We further show that the p53 RNA-binding preferences in yeast are mirrored almost exactly by a recombinant tetrameric form of the HIV-1 nucleocapsid (NC) protein thought to be a sequence-nonspecific RNA-binding protein. However, the possibility of specific RNA binding by p53 could not be ruled out because p53 and HIV-1 NC displayed certain differences in RNA-binding preference. We conclude that (1) p53 binds RNA in vivo, (2) RNA binding by p53 is largely sequence-nonspecific in the yeast nucleus, (3) some structure-specific RNA binding by p53 cannot be ruled out, and (4) caution is required when interpreting results of RNA screens in the yeast three-hybrid system because sequence-dependent differences in RNA folding and display can masquerade as sequence-dependent differences in protein recognition.
A Column-Generation Approach to the Multiple Knapsack Problem with Color Constraints
Authors: Forrest John J. H. , Kalagnanam Jayant , Ladanyi Laszlo
Published: March 2006

In this paper, we study a new problem that we refer to as the multiple knapsack with color constraints (MKCP). Motivated by a real application from the steel industry, the MKCP can be formulated by generalizing the multiple knapsack problem. A real-life instance (called mkc) of this problem class is available through MIPLIB (Bixby 2004) and a larger instance (mkc7) is downloadable from the COIN site (IBM 2004). The focus of this paper is to present improved computational results for the two mentioned instances of this problem using a column-generation approach. We solve mkc to optimality and use Dantzig-Wolfe decomposition for upper bounding the other instance. Solving mkc to optimality took less time than it takes to solve the LP relaxation of the original formulation. The larger instance is solved to near optimality (within 0.5% of optimality) in a fraction of the time required to solve the original relaxed LP.
A New Mathematical-Programming Framework for Facility-Layout Design
Authors: Anjos Miguel F. , Vannelli Anthony
Published: March 2006

We present a new framework for efficiently finding competitive solutions for the facility-layout problem. This framework is based on the combination of two new mathematical-programming models. The first model is a relaxation of the layout problem and is intended to find good starting points for the iterative algorithm used to solve the second model. The second model is an exact formulation of the facility-layout problem as a nonconvex mathematical program with equilibrium constraints (MPEC). Aspect ratio constraints, which are frequently used in facility-layout methods to restrict the occurrence of overly long and narrow departments in the computed layouts, are easily incorporated into this new framework. Finally, we present computational results showing that the complete framework can be solved efficiently using widely available optimization software, and the resulting layouts improve on those obtained using previous approaches in the literature. Moreover, the framework can be used to find different competitive layouts with relatively little computational effort, which is advantageous for a user who wishes to consider several competitive layouts rather than simply using a mathematically optimal layout.
The Distribution of Order Statistics for Discrete Random Variables with Applications to Bootstrapping
Authors: Evans Diane L. , Leemis Lawrence M. , Drew John H.
Published: March 2006

An algorithm for computing the PDF of order statistics drawn from discrete parent populations is presented, along with an implementation of the algorithm in a computer algebra system. Several examples and applications, including exact bootstrapping analysis, illustrate the utility of this algorithm. Bootstrapping procedures require that B bootstrap samples be generated in order to perform statistical inference concerning a data set. Although the requirements for the magnitude of B are typically modest, a practitioner would prefer to avoid the resampling error introduced by choosing a finite B, if possible. The part of the order-statistic algorithm for sampling with replacement from a finite sample can be used to perform exact bootstrapping analysis in certain applications, eliminating the need for replication in the analysis of a data set.
Algorithms for the Frame of a Finitely Generated Unbounded Polyhedron
Authors: Dulá José H. , López Francisco J.
Published: March 2006

Consider two finite sets 𝒜 and 𝒱 of points in m-dimensional space. The convex hull of 𝒜 and the conical hull of 𝒱 can be combined to create a finitely generated unbounded polyhedron. We explore the geometry of these polyhedral sets to design, implement, test, and compare two different algorithms for finding the frame, a minimal-cardinality subset of 𝒜 and 𝒱, that generates the same polyhedron. One algorithm is a naive approach based on the direct application of the definition of these sets. The second algorithm is based on different principles erecting the frame geometrically one element at a time. Testing indicates that the second algorithm is faster with the difference becoming increasingly dramatic as the cardinality of the sets 𝒜 and 𝒱 increases and frame density decreases.
A Metastrategy for Large-Scale Resource Management Based on Informational Decomposition
Authors: Shapiro Joel A. , Powell Warren B.
Published: March 2006

This paper addresses the solution of large, complex resource allocation problems, examples of which include large freight transportation companies and supply chain management. Some instances of these problems involve millions of constraints and tens of millions of variables. Classical formulations focus on modeling the physical problem alone. In this paper, we focus on modeling the organization of information and decisions, producing a natural decomposition based on how decisions are actually made. Restricting the size of a subproblem to the sizes of problems actually solved by real decision makers, we avoid the computational demands posed by large problems. The algorithmic challenge is producing high quality solutions that reflect the interaction between subproblems. Linear approximations have been a widely used tool for decomposition, but these can produce unstable solutions of only moderate quality. We introduce the concept of using nonlinear approximations, which creates special technical problems but also produces solutions of very high quality. The strategy is simulated on two problem classes (fleet management and supply chains) and compared against standard modeling strategies. Synchronous and asynchronous strategies are also compared.
Anti-Transglutaminase Antibody Assay of the Culture Medium of Intestinal Biopsy Specimens Can Improve the Accuracy of Celiac Disease Diagnosis
Authors: Carroccio Antonio , Di Prima Lidia , Pirrone Giuseppe , Scalici Calogero , Florena Ada M , Gasparin Maurizio , Tolazzi Giuseppe , Gucciardi Antonino , Sciumè Carmelo , Iacono Giuseppe
Published: March 2006

Background: We measured anti-transglutaminase (anti-tTG) antibody in the culture medium of intestinal biopsy specimens from patients with suspected celiac disease (CD) and evaluated the relationship between antibody production and severity of intestinal mucosal damage.

Methods: We performed diagnostic testing for CD on 273 consecutive patients. In addition to routine histologic evaluation of duodenal biopsy specimens, we assayed anti-tTG antibodies in serum and in the culture medium of duodenal biopsy specimens.

Results: CD was diagnosed in 191 of the 273 patients. Sensitivity and specificity of the serum anti-endomysium (EmA) and anti-tTG assays were 83% and 85% and 99% and 95%, respectively, and both had 88% diagnostic accuracy. EmA and anti-tTG assayed in the culture medium had 98% sensitivity, 100% specificity, and 98% diagnostic accuracy (vs serum assays; P <0.0001). Twenty-nine CD patient specimens (16%) were negative for serum anti-tTG and EmA; for 24 of these patients, anti-tTG assay of the culture medium was positive. The CD patients whose biopsy specimens were positive for serum antibodies showed the following intestinal histologies: total villous atrophy, 35%; severe villous atrophy, 25%; mild atrophy, 25%; villi with no atrophy but with increased intraepithelial lymphocytes, 15%. None of the CD patients whose specimens were negative for serum antibodies showed total or severe villous atrophy; 77% had mild villous atrophy, and 23% had no villous atrophy but had increased intraepithelial lymphocyte counts. Mild villous atrophy was also seen in specimens from ∼15% of patients without CD.

Conclusion: Anti-tTG assay of the culture medium of biopsy specimens can improve the accuracy of CD diagnosis in patients negative for serum antibodies.
Assay for Measurement of Intact B-Type Natriuretic Peptide Prohormone in Blood
Authors: Giuliani Isabelle , Rieunier François , Larue Catherine , Delagneau Jean-François , Granier Claude , Pau Bernard , Ferrière Marc , Saussine Max , Cristol Jean-Paul , Dupuy Anne-Marie , Merigeon Emmanuel , Merle Delphine , Villard Sylvie
Published: March 2006

Background: B-Type natriuretic peptide (BNP1–32) as well as the N-terminal fragment of the prohormone containing residues 1–76 (NT-proBNP1–76), both cleavage products of the precursor proBNP1–108, are reported to be powerful markers for prognosis and risk stratification of heart failure. However, the intact precursor also circulates in the bloodstream. Assays for the detection of these cleavage products have been developed, but most of these assays may overestimate the concentrations of the cleavage products because they also measure the precursor form. It is therefore important to develop an immunoassay that specifically measures solely proBNP1–108 in plasma.

Methods: After carefully designing the peptide used to immunize mice, we selected a specific monoclonal antibody (mAb Hinge76) that recognizes the cleavage site of proBNP1–108, an epitope present only in the precursor form. mAb Hinge76 recognizes recombinant proBNP1–108 in a dose-dependent manner, without any significant cross-reactivity with either recombinant NT-proBNP1–76 or synthetic BNP1–32. By combining mAb Hinge76 with a polyclonal antibody directed against BNP1–32, we were able to set up a proBNP1–108-specific sandwich immunoassay able to confirm the presence of proBNP1–108 in blood samples.

Results: From a cohort of 50 healthy persons and 170 patients with congestive heart failure (CHF), our assay was able to differentiate healthy individuals from CHF patients (P <0.005). Interestingly, plasma proBNP1–108 concentrations were correlated with New York Heart Association classification. Moreover, a close relationship between proBNP1–108 and BNP1–32 concentrations may exist, as a good correlation (r2 = 0.89) was obtained when their respective concentrations were compared.

Conclusion: mAb Hinge76 is the first proBNP1–108-specific mAb produced that allows accurate estimation of proBNP1–108 concentrations in plasma.
Frequency of Thrombophilia-Related Genetic Variations in Patients with Idiopathic Pulmonary Embolism in an Urban Emergency Department
Authors: Kruse Lori , Mitchell Alice M , Camargo Carlos A , Hernandez Jackeline , Kline Jeffrey A
Published: March 2006

Background: The frequency of the thrombophilic genetic variants factor V Leiden (FVL) G1691A, prothrombin G20210A, and methylenetetrahydrofolate reductase (MTHFR) C677T in acutely symptomatic ambulatory patients with idiopathic pulmonary embolism (PE) has not been measured.

Methods: This prospective case–control study included patients presenting to urban emergency departments (EDs) with chest pain or shortness of breath. Cases were classified as idiopathic PE (49 patients with PE, but without overt risk factors for thrombosis). Control groups included (a) patients with nonidiopathic PE (152 patients with PE and risk factors); (b) patients in whom PE was excluded (91 patients who had PE ruled out with a structured protocol, including follow-up); and (c) patients in whom PE was not suspected (193 patients without a workup for PE, who were free of PE on follow-up). Blood DNA extracts were analyzed by PCR and restriction fragment length polymorphism analysis for the FVL, prothrombin, and MTHFR sequence variations.

Results: Either the FVL or prothrombin variant was found in 10% (95% confidence interval, 3%–22%) of patients with idiopathic PE compared with 13% (8%–20%) of nonidiopathic PE, 2% (5%–14%) of PE excluded, and 9% (5%–14%) of PE not suspected patients. Patients with idiopathic PE tended to have a higher frequency of homozygous MTHFR sequence variants, but mean (SD) plasma homocysteine concentrations were not increased [15.6 (5.4) μmol/L vs 12.8 (4.6) μmol/L for homozygous, and wild-type, respectively; P = 0.40].

Conclusions: The frequency of either the FVL or prothrombin sequence variant was not increased in idiopathic PE patients compared with nonidiopathic PE patients or patients who had PE excluded. These data suggest that genotyping to detect idiopathic PE would have limited clinical utility in the urban ED setting.
Peptide Nucleic Acid–Based In Situ Hybridization Assay for Detection of Parvovirus B19 Nucleic Acids
Authors: Bonvicini Francesca , Filippone Claudia , Manaresi Elisabetta , Gentilomi Giovanna Angela , Zerbini Marialuisa , Musiani Monica , Gallinella Giorgio
Published: March 2006

Background: Peptide nucleic acid (PNA) molecules are known to bind complementary nucleic acid sequences with a much stronger affinity and with more stable binding than DNA or RNA molecules. We chose parvovirus B19, which is diagnosed by detection of nucleic acids by in situ hybridization assay (ISH) and/or PCR, as an experimental model to develop an ISH assay that uses biotinylated PNA probes to detect viral genome in clinical specimens.

Methods: We first optimized the PNA-ISH assay on B19-infected and mock-infected UT-7/EpoS1 cells and then tested the assay on archival B19 specimens and on consecutive specimens. All data were compared with data obtained with a standardized DNA-based ISH assay and confirmed by a PCR-ELISA.

Results: PNA-ISH detected B19 genome in a higher number of B19-infected UT-7/EpoS1 cells and with a more defined localization of viral nucleic acids than the standardized DNA-ISH assay. Moreover, PNA-ISH was able to detect B19 genome in all positive archival samples, whereas DNA-ISH failed in 5 samples. PNA-ISH detected more positive samples than DNA-ISH when consecutive specimens were analyzed, and a close agreement was found with PCR-ELISA results.

Conclusions: The PNA-ISH assay had sensitivity and specificity comparable to a PCR assay and was more practical and quicker to perform than standard hybridization assays. The assay may be a suitable diagnostic test for the detection of viral nucleic acids in clinical specimens.
HPLC Method for 25-Hydroxyvitamin D Measurement: Comparison with Contemporary Assays
Authors: Lensmeyer Gary L , Wiebe Donald A , Binkley Neil , Drezner Marc K
Published: March 2006

Background: The concentration of 25-hydroxyvitamin D [25(OH)D] in serum has been designated the functional indicator of vitamin D (VitD) nutritional status. Unfortunately, variability among 25(OH)D assays limits clinician ability to monitor VitD status, supplementation, and toxicity.

Methods: We developed an HPLC method that selectively measures 25-hydroxyvitamin D2 [25(OH)D2] and D3 [25(OH)D3] and compared this assay with a liquid chromatography–tandem mass spectrometry (LC-MS/MS) method, a competitive protein-binding assay (CPBA) on the Nichols Advantage™ platform, and an RIA from Diasorin.

Results: For the new HPLC assay, between-run CVs were 2.6%–4.9% for 25(OH)D3 and 3.2%–13% for 25(OH)D2; recoveries were 95%–102%; and the assay was linear from 5 μg/L to at least 200 μg/L. Comparison data were as follows: for HPLC vs LC-MS/MS, y = 1.01x − 4.82 μg/L (Sy|x = 4.93 μg/L; r = 0.996) for 25(OH)D3, and y = 0.902x − 0.566 μg/L (Sy|x = 2.56 μg/L; r = 0.9965 for 25(OH)D2; for HPLC vs Diasorin RIA, y = 0.709x − 5.86 μg/L (Sy|x = 7.35 μg/L; r = 0.7509); and for HPLC vs Nichols Advantage CPBA, y = 1.00x − 3.60 μg/L (Sy|x = 32.7 μg/L; r = 0.6823).

Conclusions: The new HPLC method is reliable, robust, and has advantages compared with the Nichols Advantage CPBA and the Diasorin RIA. The Nichols Advantage CPBA overestimated or underestimated 25(OH)D concentrations predicated on the prevailing metabolite present in patients’ sera.
Butyrylcholinesterase: Association with the Metabolic Syndrome and Identification of 2 Gene Loci Affecting Activity
Authors: Valle Anne , O’Connor Daniel T , Taylor Palmer , Zhu Gu , Montgomery Grant W , Slagboom P Eline , Martin Nicholas G , Whitfield John B
Published: March 2006

Background: Plasma cholinesterase activity is known to be correlated with plasma triglycerides, HDL- and LDL-cholesterol, and other features of the metabolic syndrome. A role in triglyceride metabolism has been proposed. Genetic variants that decrease activity have been studied extensively, but the factors contributing to overall variation in the population are poorly understood. We studied plasma cholinesterase activity in a sample of 2200 adult twins to assess covariation with cardiovascular risk factors and components of the metabolic syndrome, to determine the degree of genetic effects on enzyme activity, and to search for quantitative trait loci affecting activity.

Methods and Results: Cholinesterase activity was lower in women than in men before the age of 50, but increased to activity values similar to those in males after that age. There were highly significant correlations with variables associated with the metabolic syndrome: plasma triglyceride, HDL- and LDL-cholesterol, apolipoprotein B and E, urate, and insulin concentrations; γ-glutamyltransferase and aspartate and alanine aminotransferase activities; body mass index; and blood pressure. The heritability of plasma cholinesterase activity was 65%. Linkage analysis with data from the dizygotic twin pairs showed suggestive linkage on chromosome 3 at the location of the cholinesterase (BCHE) gene and also on chromosome 5.

Conclusions: Our results confirm and extend the connection between cholinesterase, cardiovascular risk factors, and metabolic syndrome. They establish a substantial heritability for plasma cholinesterase activity that might be attributable to variation near the structural gene and at an independent locus.
Quantitative Analysis of SRNPN Gene Methylation by Pyrosequencing as a Diagnostic Test for Prader–Willi Syndrome and Angelman Syndrome
Authors: White Helen E , Durston Victoria J , Harvey John F , Cross Nicholas CP
Published: March 2006

Background: Angelman syndrome (AS) and Prader–Willi syndrome (PWS) are 2 distinct neurodevelopmental disorders caused primarily by deficiency of specific parental contributions at an imprinted domain within the chromosomal region 15q11.2-13. In most cases, lack of paternal contribution leads to PWS either by paternal deletion (∼70%) or maternal uniparental disomy (UPD; ∼30%). Most cases of AS result from the lack of a maternal contribution from this same region by maternal deletion (∼70%) or by paternal UPD (∼5%). Analysis of allelic methylation differences at the small nuclear ribonucleoprotein polypeptide N (SNRPN) locus can differentiate the maternally and paternally inherited chromosome 15 and can be used as a diagnostic test for AS and PWS.

Methods: Sodium bisulfite–treated genomic DNA was PCR-amplified for the SNRPN gene. We used pyrosequencing to individually quantify the resulting artificial C/T sequence variation at CpG sites. Anonymized DNA samples from PWS patients (n = 40), AS patients (n = 31), and controls (n = 81) were analyzed in a blinded fashion with 2 PCR and 3 pyrosequencing reactions. We compared results from the pyrosequencing assays with those obtained with a commonly used methylation-specific PCR (MS-PCR) diagnostic protocol.

Results: The pyrosequencing assays had a sensitivity and specificity of 100% and provided quantification of methylation at 12 CpG sites within the SNRPN locus. The resulting diagnoses were 100% concordant with those obtained from the MS-PCR protocol.

Conclusions: Pyrosequencing is a rapid and robust method for quantitative methylation analysis of the SNRPN locus and can be used as a diagnostic test for PWS and AS.
Quantification of Fragments of Human Serum Inter-α-Trypsin Inhibitor Heavy Chain 4 by a Surface-Enhanced Laser Desorption/Ionization-Based Immunoassay
Authors: Song Jin , Patel Manisha , Rosenzweig C Nicole , Chan-Li Yee , Sokoll Lori J , Fung Eric T , Choi-Miura Nam-Ho , Goggins Michael , Chan Daniel W , Zhang Zhen
Published: March 2006

Background: Several proteolytically derived fragments from the proline-rich region (PRR) of human inter-α-trypsin inhibitor heavy chain 4 (ITIH4) have been identified by surface-enhanced or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS or MALDI-TOF-MS) as potential disease markers.

Methods: Previously, we developed a SELDI-based immunoassay that can simultaneously distinguish and quantify multiple isoforms/variants of a protein/peptide of interest. In this study, we used this high-throughput approach to quantify and characterize the extensive fragmentation within the PRR of human serum ITIH4 and determined its association with different disease conditions. The ITIH4-related fragments were first immunocaptured by use of beads coupled with peptide-specific antibodies. The eluates were then studied by SELDI-TOF-MS. In addition, freshly collected and immediately processed serum and plasma samples were used to analyze the ex vivo stability of these ITIH4 fragments.

Results: Human serum ITIH4 was shown to be extensively proteolytically processed within the PRR, and its fragmentation patterns were closely associated with different disease conditions. Fragmentation patterns were generally consistent with cleavages by endoprotease followed by exoprotease actions. Observed fragments changed little under different assay conditions or blood collection and processing procedures.

Conclusions: The fragmentation patterns within the PRR of human serum ITIH4 are associated with different disease conditions and may hold important diagnostic information. These fragmentation patterns could be useful as potential biomarkers for detection and classification of cancer.