bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks
Authors: Nookaew Intawat , Meechai Asawin , Thammarongtham Chinae , Laoteng Kobkul , Ruanglek Vasimon , Cheevadhanarak Supapon , Nielsen Jens , Bhumiratana Sakarindr 
Published: January 2007

AbstractWithin a metabolic network, the elementary flux modes enables a unique description of different operations of the network. Thus, the metabolic fluxes can be specified as convex combinations of the elementary flux modes. Here, we describe an approach to identify the set of elementary flux modes that operates in a given metabolic network through the use of measurements of macroscopic fluxes, that is, fluxes in and out of the cell. Besides enabling estimation of the metabolic fluxes, the parameters of the linear combinations of the elementary flux modes provide valuable physiological information; we call these parameters flux regulation coefficients (FRCs). These coefficients indicate which enzyme subsets are important at different growth conditions. We demonstrate how FRCs can be used to map the operation of the metabolic network of the yeast Saccharomyces sp. under different growth conditions. Biotechnol. Bioeng. 2007; 97: 1535–1549. © 2007 Wiley Periodicals, Inc.
Peptide tags for enhanced cellular and protein adhesion to single‐crystalline sapphire
Authors: Krauland Eric M. , Peelle Beau R. , Wittrup K. Dane , Belcher Angela M. 
Published: January 2007

AbstractIn order to facilitate a novel means for coupling proteins to metal oxides, peptides were identified from a dodecamer peptide yeast surface display library that bound a model metal oxide material, the C, A, and R crystalline faces of synthetic sapphire (α‐Al2O3). Seven rounds of screening yielded peptides enriched in basic amino acids compared to the naive library. While the C‐face had a high background of endogenous yeast cell binding, the A‐ and R faces displayed clear peptide‐mediated cell adhesion. Cell detachment assays showed that cell adhesion strength correlated positively with increasing basicity of expressed peptides. Cell adhesion was also shown to be sensitive to buffer ionic strength as well as incubation with soluble peptide (with half maximal inhibition of cell binding at ∼5 µM peptide). Next, dodecamer peptides cloned into yeast showed that lysine led to stronger interactions than arginine, and that charge distribution affected adhesion strength. We postulate binding to arise from peptide geometries that permit conformation alignment of the basic amino acids towards the surface so that the charged groups can undergo local electrostatic interactions with the surface oxide. Lastly, peptide K1 (‐(GK)6) was cloned onto the c‐terminus of maltose binding protein (MBP) and the resultant mutant protein showed a half‐maximal binding at ∼10−7–10−6M, which marked a ∼500‐ to 1,000‐fold binding improvement to sapphire's A‐face as compared with wild‐type MBP. Targeting proteins to metal oxide surfaces with peptide tags may provide a facile one‐step alternative coupling chemistry for the formation of protein bioassays and biosensors. Biotechnol. Bioeng. 2007; 97: 1009–1020. © 2007 Wiley Periodicals, Inc.
Influence of culture medium supplementation of tobacco NT1 cell suspension cultures on the N‐glycosylation of human secreted alkaline phosphatase
Authors: Becerra‐Arteaga Alejandro , Shuler Michael L. 
Published: January 2007

AbstractWe report for the first time that culture conditions, specifically culture medium supplementation with nucleotide‐sugar precursors, can alter significantly the N‐linked glycosylation of a recombinant protein in plant cell culture. Human secreted alkaline phosphatase produced in tobacco NT1 cell suspension cultures was used as a model system. Plant cell cultures were supplemented with ammonia (30 mM), galactose (1 mM) and glucosamine (10 mM) to improve the extent of N‐linked glycosylation. The highest levels of cell density and active extracellular SEAP in supplemented cultures were on average 260 g/L and 0.21 U/mL, respectively, compared to 340 g/L and 0.4 U/mL in unsupplemented cultures. The glycosylation profile of SEAP produced in supplemented cultures was determined via electrospray ionization mass spectrometry with precursor ion scanning and compared to that of SEAP produced in unsupplemented cultures. In supplemented and unsupplemented cultures, two biantennary complex‐type structures terminated with one or two N‐acetylglucosamines and one paucimannosidic glycan structure comprised about 85% of the SEAP glycan pool. These three structures contained plant‐specific xylose and fucose residues and their relative abundances were affected by each supplement. High mannose structures (6–9 mannose residues) accounted for the remaining 15% glycans in all cases. The highest proportion (approximately 66%) of a single complex‐type biantennary glycan structure terminated in both antennae by N‐ acetylglucosamine was obtained with glucosamine supplementation versus only 6% in unsupplemented medium. This structure is amenable for in vitro modification to yield a more human‐like glycan and could serve as a route to plant cell culture produced therapeutic glycoproteins. Biotechnol. Bioeng. 2007; 97: 1585–1593. © 2007 Wiley Periodicals, Inc.
Survival after hepatic resection in metastatic colorectal cancer
Authors: Cummings Linda C. , Payes Jonathan D. , Cooper Gregory S. 
Published: January 2007

AbstractBACKGROUND.Hepatectomy is the standard of care for patients with colorectal cancer who have isolated hepatic metastases; however, the long‐term survival benefits of hepatectomy in this population have not been characterized well outside of case series. For the current study, a population‐based database was used to compare the survival of patients with liver metastases from colorectal cancer who did and did not undergo hepatectomy.METHODS.Patients aged ≥65 years with incident colorectal cancer who were diagnosed from 1991 to 2001 were identified from the linked Surveillance, Epidemiology, and End Results (SEER)‐Medicare database. Liver metastasis diagnoses, colorectal resections, and hepatectomies were identified from hospital, outpatient, and physician‐supplier claims. Patients who did not undergo colorectal resection were excluded. Five‐year survival from the time of cancer diagnosis was determined by the Kaplan–Meier method. Cox proportional hazards models were used to evaluate survival.RESULTS.Among 13,599 patients who were identified with incident colorectal cancer and liver metastases, 7673 patients (56.4%) presented with stage IV disease, and the remaining patients presented with earlier stage disease and developed subsequent metastases. Only 833 patients (6.1%) in the cohort underwent hepatic resection, and their 30‐day mortality rate was 4.3%. The 5‐year survival was 32.8% among patients who underwent hepatic resection, compared with 10.5% among patients who did not undergo hepatic resection (P < .0001), and better survival was observed in the subset of patients who presented initially with disease in stages I through III. In a Cox model, which was controlled for age, sex, race, comorbidities, and stage at presentation, lack of hepatic resection was associated with a 2.78‐fold increased risk of death.CONCLUSIONS.Although hepatectomy rates among patients with colorectal cancer were low, hepatic resection was associated with improved survival. Cancer 2007 © 2007 American Cancer Society.
Intraperitoneal chemotherapy in the first‐line treatment of women with stage III epithelial ovarian cancer
Authors: Elit Laurie , Oliver Thomas K. , Covens Allan , Kwon Janice , Fung Michael Fung‐Kee , Hirte Holger W. , Oza Amit M. 
Published: January 2007

AbstractBecause women with advanced ovarian cancer have poor outcomes, it is imperative to continue exploring for novel therapies. The opportunity for intraperitoneal treatment, especially in the subgroup of patients with minimal residual disease, in which the intraperitoneal approach may have a biologic rationale for benefit over and above the standard intravenous route, needs to be explored to the fullest extent. The MEDLINE, EMBASE, and Cochrane Library databases were searched up to January 2006 for randomized trials that compared first‐line intraperitoneal‐containing chemotherapy with first‐line intravenous chemotherapy in the treatment of women with stage III epithelial ovarian cancer. Seven randomized, controlled trials were identified, including 3 large Phase III trials and 4 smaller randomized trials. The 3 large Phase III trials detected statistically significant overall survival benefits with intraperitoneal cisplatin‐containing chemotherapy compared with intravenous chemotherapy alone. The improvements in survival were 8 months, 11 months, and 16 months, respectively. Pooled analysis from 6 of the 7 randomized trials confirmed the survival effect with intraperitoneal chemotherapy compared with intravenous chemotherapy alone (relative risk, 0.88; 95% confidence interval, 0.81–0.95). Severe adverse events and catheter‐related complications with intraperitoneal chemotherapy were significantly more common and often were dose‐limiting. The results from this review indicated that cisplatin‐containing intraperitoneal chemotherapy should be offered to patients on the basis of significant improvements in overall survival. The appropriate clinical and institutional multidisciplinary facilities are needed for the safe delivery of this treatment in optimally debulked patients. Further research is needed concerning specific aspects of the treatment, such as optimal agent, dose, and scheduling. Cancer 2007;109:692–702. © 2007 American Cancer Society.
Testicular cancer mortality in the Americas, 1980–2003
Authors: Bertuccio Paola , Malvezzi Matteo , Chatenoud Liliane , Bosetti Cristina , Negri Eva , Levi Fabio , La Vecchia Carlo 
Published: January 2007

AbstractBACKGROUND.Testicular cancer is generally curable if appropriate treatment is given. Data and statistics on testicular cancer mortality over the last decades are available from the US and Canada, but are more difficult to find, in a standard and comparable format, for Central and South American countries. The objective of the study was to compare death rates and trends over the 1980–2003 period in all the American countries that provide data.METHODS.Overall and 20 to 44 years age‐standardized (world population) mortality rates from testicular cancer, derived from the World Health Organization (WHO) database, are presented for the most recent available calendar years in 10 American countries. Trends in mortality for selected countries of the Americas are also given over the period 1980–2003.RESULTS.In the early 1980s the highest testicular cancer mortality rates were observed in Chile (1.7/100,000 at all ages, 3.6/100,000 at 20–44 years) and Argentina (0.9/100,000 at all ages, 1.7/100,000 at 20–44 years), as compared with 0.4/100,000 for all ages and 0.6/100,000 at 20 to 44 years in Canada, and 0.3/100,000 for all ages and 0.7/100,000 at 20 to 44 years in the US. In 2001–2003, testicular cancer mortality had fallen to 0.2/100,000 in men aged 20 to 44 years in Canada, and to 0.4/100,000 in the US. Conversely, rates were still 1.6/100,000 in Argentina, 2.2/100,000 in Chile and 1.2/100,000 in Mexico, and were around 0.5–0.6/100,000 in most other Latin American countries that provide data.CONCLUSIONS.Mortality from testicular cancer in (young) men remains exceedingly high in most Latin American countries. Urgent intervention is required to provide treatment (essentially modern integrated platinum‐based chemotherapy) for this largely curable neoplasm in young men. Cancer 2007 © 2007 American Cancer Society.
Brain tumors in individuals with familial adenomatous polyposis
Authors: Attard Thomas M. , Giglio Pierre , Koppula Sireesha , Snyder Carrie , Lynch Henry T. 
Published: January 2007

AbstractBACKGROUND.Most individuals with Familial Adenomatous Polyposis (FAP) harbor mutations in the APC gene on chromosome 5q21. They are at an increased risk of brain tumors, including cerebellar medulloblastoma, when compared with the general population (Brain Tumor Polyposis—BTP Type 2). Genotype‐phenotype correlations between APC gene mutations and central nervous system (CNS) tumors have, thus far not been successful. Herein the authors have pooled their registry experience in BTP type 2 with the published reports.METHODS.The authors analyzed their established hereditary CRC Registry for brain tumors in FAP pedigrees (56 families, 213 individuals), pooled their patients with BTP and known APC mutations with those reported thus far elsewhere, and compared the resulting mutation distribution of FAP‐BTP with the mutation distribution for APC mutations in the US.RESULTS.Twenty‐eight patients from 24 families were accrued, the most common brain tumor in BTP was medulloblastoma (60%) predominantly in females (12:5) under the age of 20 (mean age 14.7 SD 9.2). Other histologic subtypes included astrocytoma and ependymoma. Analysis of the pooled APC mutation data by Chi‐square test of association shows an odds ratio of 3.7 (P < .005) for all brain tumor subtypes and 13.1 (P < .001) for medulloblastoma in patients harboring segment 2 APC mutation (codons 679–1224) compared to nonsegment 2 mutation.CONCLUSIONS.In patients with FAP and identifiable APC gene mutation, CNS tumors, especially medulloblastoma which developed in most cases during childhood, are more common in females with FAP and APC gene mutation in codons 686–1217. Further studies are necessary to determine if this observation and the natural history of medulloblastoma in children justifies novel, aggressive, targeted screening of at—risk individuals. Cancer 2007 © 2007 American Cancer Society.
Abnormalities of epidermal growth factor receptor in lung squamous‐cell carcinomas, adenosquamous carcinomas, and large‐cell carcinomas
Authors: Ohtsuka Kouki , Ohnishi Hiroaki , Fujiwara Masachika , Kishino Tomonori , Matsushima Satsuki , Furuyashiki Go , Takei Hidefumi , Koshiishi Yoshihiko , Goya Tomoyuki , Watanabe Takashi 
Published: January 2007

AbstractBACKGROUND.Tyrosine kinase domain (TKD) gene mutations of the epidermal growth factor receptor gene (EGFR) have proven to be clinically significant in nonsmall‐cell lung cancer (NSCLC), particularly in adenocarcinoma. However, TKD mutations together with deletion mutations in the extracellular domain of EGFR (EGFRvIII) have not been fully investigated in NSCLC except for adenocarcinoma. The present study sought to gain further insight into the significance of EGFR mutations in NSCLC by focusing on nonadenocarcinoma NSCLC.METHODS.EGFR TKD mutations were investigated using direct sequencing and mutation‐specific polymerase chain reaction (PCR), and EGFRvIII mutations were examined using reverse transcriptase‐PCR in samples from 42 NSCLC patients and 6 NSCLC cell lines excluding adenocarcinoma.RESULTS.EGFR TKD mutations were detected in 1 of 7 (14%) squamous‐cell carcinomas with an adenocarcinoma component and 2 of 4 (50%) adenosquamous carcinomas. In contrast, EGFR TKD mutations were not identified in 24 pure squamous‐cell carcinomas without any adenocarcinoma component, 7 large‐cell carcinomas, or 6 cell lines. EGFRvIII was detected solely in 1 of 7 large‐cell carcinomas (14%), but not in 31 squamous‐cell carcinomas, 4 adenosquamous carcinomas, or 6 cell lines.CONCLUSIONS.These results suggest that EGFR TKD mutations are found in NSCLCs with an adenocarcinoma element. Patients with such lesions are thus considered candidates for molecular therapies targeting EGFR. Cancer 2007 © 2007 American Cancer Society.
Sequential chemotherapy in nonsmall‐cell lung cancer
Authors: Ceribelli Anna , Pino Maria S. , Gelibter Alain J. , Milella Michele , Cecere Fabiana L. , Caterino Mauro , Facciolo Francesco , Mirri Alessandra , Cognetti Francesco 
Published: January 2007

AbstractBACKGROUND.Improving results in nonsmall‐cell lung cancer (NSCLC) will require the development of new drugs and strategies to combine available agents. On the basis of data indicating the activity of docetaxel as second‐line therapy, a Phase II study was conducted to evaluate the efficacy and toxicity of the sequential combination of chemotherapy consisting of cisplatin (P) and gemcitabine (G) followed by docetaxel (DOC) in patients with advanced NSCLC.METHODS.Patients with 1997 TNM stage IIIB (pleural effusion)/stage IV NSCLC, performance status (PS) of 0–1, and normal organ function were eligible. Therapy consisted of P at 75 mg/m2 on Day 1 and G 1200 mg/m2 on Days 1 and 8 every 3 weeks for 3 cycles followed, in nonprogressive patients, by DOC 30 mg/m2 every week for 6 consecutive weeks every 8 weeks for 2 cycles.RESULTS.Fifty‐two eligible patients were enrolled (M/F, 39/13; stage IIIB/IV, 8/44; PS 0, 73%, PS 1, 27%; median age, 58 years; range, 36–73). The overall response rate was 36.5% (95% confidence interval [CI]: 23–49). The median overall survival was 11 months (95% CI: 9–13); the median progression‐free survival was 6 months (95% CI: 5–7); and the 1‐ and 2‐year survivals were 48% and 25%, respectively. One‐ and 2‐year progression‐free survivals were 12% and 8%, respectively. Both phases of the treatment protocol were well tolerated.CONCLUSIONS.P/G followed by weekly DOC is well tolerated and active as first‐line therapy for NSCLC patients and provides a feasible chemotherapeutic option in this clinical setting. Cancer 2007 © 2007 American Cancer Society.
Clinical outcome of patients with Ewing sarcoma family of tumors of bone in Japan
Authors: Obata Hideto , Ueda Takafumi , Kawai Akira , Ishii Takeshi , Ozaki Toshifumi , Abe Satoshi , Tanaka Kazuhiro , Tsuchiya Hiroyuki , Matsumine Akihiko , Yabe Hiroo 
Published: January 2007

AbstractBACKGROUND.Ewing sarcoma family of tumors (ESFT) of bone is extremely rare in Japan. The objectives of the current study were to assess the clinical outcome and prognostic factors of patients with ESFT of bone in Japan and to compare them between Euro‐American and Japanese populations.METHODS.The authors conducted a retrospective analysis of 243 patients who were treated for ESFT of bone in Japan between 1981 and 2003. Local therapy was surgery in 35% of patients, surgery combined with radiotherapy in 40% of patients, radiotherapy alone in 22% of patients, and no local treatment in 3% of patients. All but 3 patients received various regimens of multidrug chemotherapy.RESULTS.The median patient age was 16 years. The primary disease sites were the trunk in 53% of patients and the extremities in 47% of patients. Forty‐one patients had metastases at presentation. The median follow‐up was 66 months. A univariate survival analysis demonstrated that patients who had metastases at presentation, primary site in the trunk, age ≥16 years, tumor size ≥10 cm, tumor that responded poorly to induction chemotherapy, and local treatment with radiotherapy alone had a significantly worse event‐free survival (EFS). A multivariate analysis further verified that the former 3 factors were significant adverse prognostic factors. Of 201 patients with localized disease, 45 patients who received current chemotherapy regimens that included ifosfamide and etoposide had a significantly better 5‐year EFS rate (67.6%) compared with other patients.CONCLUSIONS.The clinical outcome of patients with localized ESFT of bone in Japan has improved markedly with the use of current chemotherapy regimens that include ifosfamide and etoposide and has become comparable to the outcomes observed in other major series of Euro‐American patients. The prognostic factors are also almost identical. Cancer 2007 © 2007 American Cancer Society.
Production of activated carbon by H3PO4 activation treatment of corncob and its performance in removing nitrobenzene from water
Authors: Sun Yong , Zhang Jin‐Ping , Yang Gang , Li Zuo‐Hu 
Published: January 2007

AbstractActivated carbon was produced by fast precarbonization of corncobs in a fluidized bed followed by H3PO4 activation. The results showed that the product is essentially microporous carbon whose BET surface area and pore volume when the carbon was activated at 900°C were 1588 m2/g and 0.8163 mL/g, respectively. The experimental operating conditions were as follows: carbonizing the corncobs in the preheated fluidized‐bed at 350°C for 5 min using N2 as carrier gas; impregnating the char with H3PO4 with an impregnation ratio of 1:5 (Char/H3PO4); and activating the mixture at 900°C for 30 min in the tubular furnace. The potential usefulness of the resultant carbons for removal of nitrobenzene from water was also investigated. © 2007 American Institute of Chemical Engineers Environ Prog 26:78–85, 2007.
Soil properties and perceived disturbance of grasslands subjected to mechanized military training: evaluation of an index
Authors: Althoff D. P. , Althoff P. S. , Lambrecht N. D. , Gipson P. S. , Pontius J. S. , Woodford P. B. 
Published: January 2007

AbstractMechanized maneuver training impacts the landscape by creating depressions, compacting soils, producing bare ground areas, transporting seeds of invasive plants, and crushing vegetation. We measured 3 physical, 13 chemical, and 2 biological soil properties and used a disturbance index (DI) based on perceptions of soil conditions on a military installation to assess the condition of 100 × 100 m plots (1 ha): 10 in 2002 and 10 in 2004. Potential DI scores range from 0 (no appreciable evidence of disturbance) to 1 (>95 per cent of the plot disturbed). Bulk density, porosity (%), and water content (%)—all at 5·1–10·0 cm depth, and nematode family richness (NFR) were significantly, negatively correlated (Spearman coefficients, rs) with the DI of both years. The strong negative correlation (rs = −0·69 in 2002, −0·79 in 2004) of NFR with the DI appears to reflect the status of nematode diversity and, therefore, may serve as a useful, inexpensive approach to rapidly assessing grasslands subjected to mechanized military training. Copyright © 2007 John Wiley & Sons, Ltd.