bluuebunny/crossref_metadata_2025 huggingface dataset:
Subcutaneous tri‐block copolymer produces recovery from spinal cord injury
Authors: Borgens Richard B. , Bohnert Debbie , Duerstock Brad , Spomar Daniel , Lee Raphael C.
Published: March 2004

We have studied the ability of nonionic detergents and hydrophilic polymers to seal permeabilized membranes of damaged cells, rescuing them from progressive dissolution, degeneration, and death. We report that a single subcutaneous injection of the tri‐block copolymer, Poloxamer 188 (P188) 6 hr after a severe compression of the adult guinea pig spinal cord is able to: (1) preserve the anatomic integrity of the cord; (2) produce a rapid recovery of nerve impulse conduction through the lesion; and (3) produce a behavioral recovery of a spinal cord dependent long tract spinal cord reflex. These observations stood out against a control group in blinded evaluation. Conduction through the lesion was monitored by stimulating the tibial nerve of the hind limb, and measuring the arrival of evoked potentials at the contralateral sensory cortex of the brain (somatosensory evoked potentials; SSEP). Behavioral recovery was determined by a return of sensitivity of formerly areflexic receptive fields of the cutaneous trunchi muscle (CTM) reflex. This contraction of back skin in response to tactile stimulation is totally dependent on the integrity of an identified bilateral column of ascending long tract axons. A statistically significant recovery of both SSEP conduction through the lesion and the CTM reflex occurred in P188‐treated animals compared to vehicle‐treated controls. Quantitative 3D computer reconstruction of the lesioned vertebral segment of spinal cord revealed a statistically significant sparing of spinal cord parenchyma and a significant reduction in cavitation of the spinal cord compared to control animals We determined that the proportion of P188‐treated animals that recovered evoked potentials were nearly identical to that produced by a subcutaneous injection of polyethylene glycol (PEG). In contrast, P188 was not as effective as PEG in producing a recovery of CTM functioning. We discuss the likely differences in the mechanisms of action of these two polymers, and the possibilities inherent in a combined treatment. © 2004 Wiley‐Liss, Inc.
Arc interacts with microtubules/microtubule‐associated protein 2 and attenuates microtubule‐associated protein 2 immunoreactivity in the dendrites
Authors: Fujimoto Takahiro , Tanaka Hidekazu , Kumamaru Emi , Okamura Ko , Miki Naomasa
Published: March 2004

Arc, activity‐regulated cytoskeleton‐associated gene, is an immediate early gene, and its expression is regulated by a variety of stimuli, such as electric stimulation and methamphetamine. The function of Arc, however, is unknown. To explore this function, we carried out expression experiments by transfecting green fluorescent protein (GFP)‐Arc constructs or by using a protein transduction system in hippocampal cultured neurons. We found that the overexpression of Arc as well as Arc induction by seizure in vivo decreased microtubule‐associated protein 2 (MAP2) staining in the dendrites by immunocytochemistry, although MAP2 content was not changed on Western blot. Furthermore, Arc interacted with newly polymerized microtubules and MAP2, leading to blocking of the epitope of MAP2. The data suggest that Arc increased by synaptic activities would trigger dendritic remodeling by interacting with cytoskeletal proteins. © 2004 Wiley‐Liss, Inc.
Specificity of regulatory CD4+CD25+ T cells for self‐T cell receptor determinants
Authors: Buenafe Abigail C. , Tsaknaridis Laura , Spencer Leslie , Hicks Kevin S. , McMahan Rachel H. , Watson Lisa , Culbertson Nicole E. , Latocha Dorian , Wegmann Keith , Finn Tom , Bartholomew Richard , Burrows Gregory G. , Whitham Ruth , Bourdette Dennis N. , Jones Richard E. , Offner Halina , Chou Yuan K. , Vandenbark Arthur A.
Published: March 2004

Although the phenotypic and regulatory properties of the CD4+CD25+ T cell lineage (Treg cells) have been well described, the specificities remain largely unknown. We demonstrate here that the CD4+CD25+ Treg population includes the recognition of a broad spectrum of human TCR CDR2 determinants found in the germline V gene repertoire as well as that of a clonotypic nongermline‐encoded CDR3β sequence present in a recombinant soluble T cell receptor (TCR) protein. Regulatory activity was demonstrated in T cell lines responsive to TCR but not in T cell lines responsive to control antigens. Inhibitory activity of TCR‐reactive T cells required cell–cell contact and involved CTLA‐4, GITR, IL‐10, and IL‐17. Thus, the T–T regulatory network includes Treg cells with specificity directed toward self‐TCR determinants. © 2004 Wiley‐Liss, Inc.
Expression of eukaryotic initiation factor 4E in gastric adenocarcinoma and its association with clinical outcome
Authors: Chen Chiung‐Nien , Hsieh Fon‐Jou , Cheng Yung‐Ming , Lee Po‐Huang , Chang King‐Jen
Published: March 2004

Background and Objectives

Overexpression of eIF4E can result in oncogenic transformation and uncontrolled growth of mammalian cells, presumably by facilitating the expression of growth‐control gene products, which are normally translationally repressed. Overexpression of eIF4E was present in human breast carcinoma and human head and neck squamous cell carcinoma, and may be of prognostic value in breast carcinomas. In order to elucidate the clinical significance of eIF4E expression, this study was conducted to quantify expression of eIF4E in human gastric cancer tissue and correlate them with clinicopathological factors and patient survival.

Methods

Specimens from sixty‐nine patients with gastric adenocarcinoma were analyzed and eIF4E overexpression was quantified by Western blot analysis. Quantification of eIF4E levels in cancer was expressed relative to controls from non‐tumorous mucosa of the same patients. Confirmation of eIF4E overexpression at the cellular level was performed using immunohistochemical staining. The association of clinicopathologic factors and survival with eIF4E expression was analyzed.

Results

In non‐tumorous parts of specimens, overexpression of eIF4E was always present in gastric glands but not in gastric pits lining mucosa, and it was also expressed in the areas of intestinal metaplasia and dysplasia. In the 69 specimens, the mean eIF4E expression was 5.77 ± 8.55‐fold (mean ± standard deviation), ranged from from 0.1‐fold to 38‐fold. The degree of eIF4E expression appeared to be independent of invasion depth of tumor, lymph node metastasis, Lauren classification, Borrmann types, and Helicobacter pylori infection. Marked overexpression of eIF4E (more than seven‐fold) was correlated with tumor vascular invasion (P = 0.046, Fisher exact‐test). The survival rate of the patients with underexpression or mild overexpression of eIF4E (less than sevenfold) was significantly higher than that with marked eIF4E overexpression (more than sevenfold) (P = 0.01734, log rank test).

Conclusions

Marked eIF4E overexpression in gastric cancer was found to be associated with vascular invasion. The prognosis for gastric cancer patients with marked overexpression of eIF4E was worse than those with underexpression. It may serve as an additional prognostic and therapeutic factor in gastric cancer, and deserves further investigation. J. Surg. Oncol. 2004;86:22–27. © 2004 Wiley‐Liss, Inc.
Clinically aggressive pseudomyxoma peritonei: A variant of a histologically indolent process
Authors: Mohamed Faheez , Gething Sue , Haiba Moutaz , Brun Erwin A. , Sugarbaker Paul H.
Published: March 2004

Background

Three distinct morphologic types of pseudomyxoma peritonei syndrome have been defined: disseminated peritoneal adenomucinosis (DPAM), peritoneal mucinous carcinoma (PMCA), and a hybrid morphologic type. Prognosis is best in patients with DPAM; unfortunately, some patients with DPAM succumb to a rapidly progressive disease process.

Methods

We identified a subset of 11 patients with a histopathology of DPAM but a clinical course showing an invasive disease process. As a comparison group, from a database of 501 patients with pseudomyxoma peritonei, we selected 22 age‐ and sex‐matched controls with a DPAM histology who are alive with no evidence of disease. Clinical factors were identified for comparison of case and control groups. Expression of mucin antigens, mucin (MUC)1 and MUC2, were evaluated using immunohistochemistry.

Results

The study group consisted of 11 patients (five men and six women), with a median survival of 52.2 months (SD 7.46) and a 31% 5‐year survival. All 22 matched control cases (10 men and 12 women) are alive and disease‐free. Clinical data on the study and control groups including co‐morbidity were similar. No significant difference in the expression of MUC1 (P = 0.74, Fisher's exact test) or MUC2 (P = 0.34, Fisher's exact test) was demonstrated between groups.

Conclusions

Further investigation of pseudomyxoma peritonei at a molecular and genetic level may help to formulate a more comprehensive classification. J. Surg. Oncol. 2004;86:10–15. © 2004 Wiley‐Liss, Inc.
Reconstruction of early lower gingivo buccal complex lesions using floor of mouth advancement augmented with hyoglossus release
Authors: Pai Prathamesh S. , Chaturvedi Pankaj , D'Cruz Anil K. , Chaukar Devendra A. , Pathak Kumar Alok , Deshpande Mandar S. , Kar Dilip K.
Published: March 2004

The surgical treatment in early cancers of the lower gingivobuccal (GB) complex involves wide resection of the buccal mucosa and GB sulcus with or without marginal mandibulectomy. To reconstruct this defect we endeavour to describe a method of advancement of the lateral floor of mouth and tongue to provide pliable, vascularised tissue to bridge the mucosal defect and achieve tension free, primary closure whilst preserving maximum tongue mobility and maintaining adequate mouth opening, thus offering an elegant and simple solution to the problems of reconstruction in early lesions of the lower gingivo buccal complex. J. Surg. Oncol. 2004;86:41–43. © 2004 Wiley‐Liss, Inc.
Prognostic value of cytosolyc cathepsin D content in resectable gastric cancer
Authors: Manuel del Casar José , Vizoso Francisco José , Abdel‐Laa Omar , Sanz Lourdes , Martín Aranzazu , Daniela Corte María , Bongera Miguel , García Muñiz José Luis , Fueyo Antonio
Published: March 2004

Background and Aims

Cathepsin D (Cath‐D) is an aspartyl protease involved in protein catabolism and tissue remodelling. In the present article, we evaluate the tumor content of Cath‐D in resectable gastric carcinomas and its relation with clinical and pathological parameters, as well as its prognostic significance.

Method

This prospective study included a series of 60 patients with primary gastric adenocarcinoma, who first underwent a complete surgical resection of their tumors and then were evaluated for disease recurrence and survival status during a mean follow‐up period of 41.5 months. Cath D was measured in cytosolic samples using an immune‐radiometric assay which determined the total amount of Cath‐D (52K, 48K, and 34K).

Results

The tumor content of Cath‐D ranged from 4 to 247 pmol/mg protein and from 6.4 to 97.7 pmol/mg protein in adjacent non‐neoplastic mucosa samples. Cytosolic Cath‐D levels were significantly higher in neoplastic tissues (P < 0.001). Statistical analysis also demonstrated that younger patients showed lower Cath‐D tumor levels than older ones. Likewise, patients with lower tumor levels of Cath‐D had better survival than those with intermediate or high Cath‐D tumor content (P = 0.002). This finding showed an independent prognostic value on survival (P = 0.02).

Conclusions

The present study demonstrates the presence of higher Cath‐D content in gastric carcinomas than in adjacent non‐neoplastic mucosa, and that high intratumor Cath‐D levels indentify a subgroup of resectable gastric cancer patients with a high probability of relapse as well as worse survival. J. Surg. Oncol. 2004;86:16–21. © 2004 Wiley‐Liss, Inc.
A review of thyroid cancer with intermediate differentiation
Authors: Sywak Mark , Pasieka Janice L. , Ogilvie Travis
Published: March 2004

Background and Objectives

Tall cell (TCV), columnar cell (CCV), insular (IC), diffuse sclerosing (DSPTC) and solid/trabecular are uncommon subtypes of thyroid cancer, which have generally been described in case reports or small series in the world literature. Due to the rarity of these thyroid cancers, their clinical behavior remains incompletely understood. The aim of this review was to pool the currently available clinical information regarding these uncommon thyroid cancers so as to gain a better understanding of their clinical aspects and natural history.

Methods

A computer‐aided search of MEDLINE (1966–2001, PUBMED website) and CINAHL (1982–2001) databases was performed, as well as a review of the reference section of each primary study was done. All cases of TCV, CCV, DSPTC, solid/trabecular, and IC described in the English medical literature were identified. For the subtypes DSPTC, TCV, and IC, clinical data from the published case series were combined in a weighted analysis. Weighting was based on the number of cases per series. For the CCV and the solid/trabecular variant, due to the small number of cases, raw figures for the clinical features were obtained.

Results

DSPTC (n = 65) appeared to have a tendency for intra‐thyroidal extension (40%) and a high propensity for nodal metastates (68%). The mean overall tumor related mortality was similar to well differentiated thyroid cancer (WDTC) at only 2% at 8 years follow‐up. The solid/trabecular variant was seen in 37% of the radiation induced thyroid tumors of the Chernobyl accident. It had a high propensity for extrathyroidal extension, and cervical lymph node metastases were found in up to 83% of patients. Unlike WDTC, TCV (n = 209) was a more aggressive tumor, associated with distant metastases in 22% of cases and had a mean tumor related mortality of 16%. The histological diagnosis of TCV was a poor prognostic factor regardless of patient age or tumor size. The CCV (n = 41) had a high overall mortality rate of 32%. When encapsulated, however, CCV had an excellent prognosis similar to that found in WDTC. In contrast, CCV tumors that were not encapsulated had extrathyroidal spread in 67% and had distant metastases in 87% of patients. The variant of IC (n = 213) appeared to be an aggressive subtype of thyroid cancer. The mean loco‐regional recurrence and/or distant metastases rate was 64% and tumor related mortality was high at 32%.

Conclusions

DSPTC, TCV, CCV, and IC are thyroid cancer subtypes, which have a biological aggressiveness, which appear to be intermediate between that of WDTC and poorly differentiated anaplastic thyroid cancer. J. Surg. Oncol. 2004;86:44–54. © 2004 Wiley‐Liss, Inc.
Recurrence of hepatocellular carcinoma after liver transplant: Patterns and prognosis
Authors: Roayaie Sasan , Schwartz Jonathan D. , Sung Max W. , Emre Sukru H. , Miller Charles M. , Gondolesi Gabriel E. , Krieger Nancy R. , Schwartz Myron E.
Published: March 2004

Very little is known about the natural history, effects of therapy, and survival after recurrence of hepatocellular carcinoma (HCC) after liver transplantation. All adult patients undergoing liver transplant from September 19, 1988, until September 19, 2002, were reviewed. Only patients with histologically proven HCC in the explant who subsequently developed recurrence were included in further analysis. The endpoints analyzed were survival from time of transplant and survival from time of recurrence. Recipient demographics and laboratory values, technique of transplant (whole cadaver, split, or living donor), and tumor characteristics were analyzed. The time to, location of, and any medical or surgical treatment of recurrences also were considered. Of the 311 patients with HCC in the explant, 57 (18.3%) eventually were diagnosed with recurrent tumor after transplant. Median time to recurrence was 12.3. Five-year survival was significantly lower for patients with recurrence (22%) than for patients without recurrence (64%)(P < 0.0001). Multivariate analysis demonstrated that the size and differentiation of the original tumor, as well as the presence of bone recurrence, were independently associated with survival from transplant in patients with recurrence. When survival from the time of recurrence was analyzed, multivariate analysis showed that the absence of bone metastases, recurrence more than 12 months from transplant, and surgical treatment of the recurrence were independently associated with significantly longer survival. In conclusion, recurrence of HCC significantly shortens survival after transplant. Nonetheless, some patients with recurrence can be expected to live for a considerable period of time. Recurrent disease should be treated surgically when possible, because surgery is independently associated with longer survival. (Liver Transpl 2004;10:534-540.)
Modified two‐probe approach for amplitude‐only near‐field measurements
Authors: El‐Said Yaser S. , Attiya Ahmed M.
Published: March 2004

A simple, effective technique for phase retrieval of antenna near‐field measurements is presented. This technique is based on using two similar scanning probes to collect four scalar near‐field measurements simultaneously, namely, the squared voltages received by two probes, the squared value of the summation of the received voltages by the two probes in phase, and the squared value of the summation of the received voltages by the two probes shifted by an arbitrarily known phase shift. A simple relation is used to retrieve the phase distribution by utilizing these four scalar measurements. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 270–273, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20114
High‐quality‐factor (33) and high‐resonant‐frequency (35 GHz) spiral inductors fabricated in 0.25‐μM mixed‐signal/RF‐CMOS technology
Authors: Lin Yo‐Sheng , Wu Shen‐Hong , Chiu Hong‐Wei , Lu Shey‐Shi
Published: March 2004

In this paper, we demonstrate a comprehensive analysis of the effects of the layout, temperature (from −50°C to 200°C), top‐metal‐layer thickness, and substrate impedance on the performances of high‐quality‐factor (Qfactor) and high‐resonant‐frequency (fSR) spiral inductors with 6‐μm‐thick top metal in 0.25‐μm CMOS technology for radio‐frequency integrated‐circuit (RF‐IC) applications. We found thatQfactor decreases with increasing temperature but shows a reverse behavior at a higher‐frequency range, while NF increases with increasing temperature but shows a reverse behavior within a higher‐frequency range. This phenomenon can be explained by the positive‐temperature coefficients of the metal series resistance (Rs) and the substrate resistance (Rsub). In addition, the proton bombardment post‐process can largely increase the maximumQfactor (Qmax) of the inductors, mainly due to the increase of substrate impedance. The present analysis enables RF engineers to understand more deeply the temperature and substrate impedance dependences of the spiral inductors fabricated on a silicon substrate. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 276–279, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20117
Effect of losses and dispersion on the focusing properties of left‐handed media
Authors: Marqués R. , Baena J.
Published: March 2004

By means of an analysis of the field radiated by a point source placed in front of an infinite left‐handed slab, the effect off losses and dispersion on the focusing properties of continuous left‐handed media are analyzed. It is shown that subwavelength focusing of point‐like quasi‐monochromatic sources can be achieved by using physical left‐handed slabs, provided some conditions are fulfilled. These conditions are qualitative and quantitatively analyzed. Numerical examples that show the accuracy of this analysis are provided. Finally, the proposed electromagnetic analysis and the geometrical Veselago's demonstration of over‐wavelength focusing by left‐handed slabs are found to be mutually consistent. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 290–294, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20119
Field trial of the 40 Gb/s ETDM prototype over 219 km of the installed single‐mode fiber
Authors: Lee San Soo , Cho Hyun Woo , Lim Sang‐Kyu , Han Ki Ho , Han Jin Soo , Chu Moo Jung , Ko Je Soo , Yoon Kyeong‐Mo , Lee Yong‐Gi
Published: March 2004

We demonstrate a field trial of the 40 Gb/s single‐channel electrical time‐division multiplexing (ETDM) prototype by using KT's installed single‐mode fiber (SMF). The prototype consists of a 40‐Gb/s optical transmitter, receiver, and four sets of optical amplifiers. In order to provide a practical and economical field trial, we adopt conventional erbium‐doped fiber amplifiers (EDFAs) and precise dispersion compensation technology. We obtain the power penalties of 0.5 dB for 10 Gb/s tributary channels after transmission of 219 km. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 304–306, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20123
Optimization of slicing level in an OC‐192 receiver
Authors: Cheng D.
Published: March 2004

Based on the ratio of noise‐dependent to signal‐independent noise, the slicing level of a decision circuit in the OC‐192 receiver is optimized. The impact of the slicing level on bit‐error rate (BER) is illustrated for different fade margins and noise‐dependent to signal‐independent noise ratio. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 310–312, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20125
A new condition to identify isotropic dielectric‐magnetic materials displaying negative phase velocity
Authors: Depine Ricardo A. , Lakhtakia Akhlesh
Published: March 2004

The derivation of a new condition for characterizing isotropic dielectric‐magnetic materials exhibiting negative phase velocity, and the equivalence of that condition with previously derived conditions, are presented. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 315–316, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20127
High‐gain triple‐pass amplification in two‐stage optical amplifier architecture
Authors: Khairi Khairil A. , Naji Ahmed W. , Sheih S‐J , Mahdi Mohd A.
Published: March 2004

A new high‐gain Erbium‐doped fiber amplifier configured in a dual‐stage triple‐pass amplification scheme is presented. The first‐stage amplifier consists of double‐pass amplification in order to obtain high gain, while the second‐stage amplifier is single‐pass amplification. The optimum pump ratio of the first‐stage pump laser to the total pump power is found to be 30%. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 317–318, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20128
Maxwellian circuits and Green's functions
Authors: Leung K. W. , Liu Y. W. , Yang P. , Mei K. K.
Published: March 2004

In a series of conference and journal papers [1–3], Mei has laid the foundation of the theory of Maxwellian circuits, which asserts that any wire structure, such as a thin wire antenna or a microstrip device, can be represented by an equivalent circuit, the solution of which is identical to the solution of the Maxwell equations of the structure. Such a circuit is said to be Maxwellian. This paper investigates the environmental effects of the Maxwellian circuit, in particular the role of the Green's functions of the integral equation. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 318–320, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20129
The role of caregiver gender and caregiver burden in nursing home placements for elderly Taiwanese survivors of stroke
Authors: Kao Hsueh‐Fen S. , McHugh Mary L.
Published: March 2004

The role of caregiver gender in caregiver burden and the association between the level of caregiver burden and institutionalization of elderly stroke survivors in Taiwan were explored using a correlational, descriptive design. The convenience sample was composed of 78 male and 69 female primary caregivers of stroke survivors. Simple multiple regression and t tests were used to test the research questions. Women perceived caregiving as more burdensome than men did. Caregiver burden was most strongly associated with the characteristics of the care recipients and with institutionalization. The proposed model explained 45% and 28% of the variance in caregiver burden for male and female caregivers, respectively. It is recommended that the professional nursing role in Taiwan be expanded to include postdischarge care, respite, and home‐care services to allow families to keep their elderly at home as long as possible and to provide culturally sensitive care to families that might be traumatized by having to violate ethnic Chinese cultural norms by institutionalizing family members. © 2004 Wiley Periodicals, Inc. Res Nurs Health 27:121–134, 2004
Alzheimer's disease caregiving information and skills, part III: Group process issues and concerns
Authors: Perraud Suzanne , Farran Carol J. , Loukissa Dimitra , Paun Olimpia
Published: March 2004

In this descriptive study we examined content and processes in a group‐based component of an ongoing clinical trial with family caregivers of persons with dementia. The purpose was to identify issues arising from the group processes that could be used to inform future skill‐building caregiver groups. Summaries from two types of intervention groups, a caregiver skill‐building (CSB) treatment intervention and an information and support only (ISO) control intervention were examined, along with data collected during a group leader debriefing session. Three major categories of process information were identified: (a) group member behaviors that support group processes necessary for skill development, (b) group leader behaviors that support group processes necessary for skill development, and (c) the phases of learning in caregiver (CG) skill development. Subcategories and specific content in each of these areas are identified in this article, and a list of member and leader behaviors that might support future skill development in groups is presented. © 2004 Wiley Periodicals, Inc. Res Nurs Health 27:110–120, 2004
Identification of circulating antibodies to tumor‐associated proteins for combined use as markers of non‐small cell lung cancer
Authors: Zhong Li , Peng Xuejun , Hidalgo Giovanna E. , Doherty Dennis E. , Stromberg Arnold J. , Hirschowitz Edward A.
Published: March 2004

Currently only a limited number of tumor markers for non‐small cell lung cancer (NSCLC) are available. Antibodies to tumor‐associated proteins may expand the number of available tumor markers for lung cancer and be used together in a serum profile to enhance sensitivity and specificity. In this study, we isolated 57 tumor‐associated proteins from two NSCLC cDNA T7 phage libraries using biopan enrichment techniques with NSCLC patient and normal sera. Sequence analysis showed that among the 57 phage‐displayed proteins 45 have sequence identity with known or putative tumor‐associated proteins. Immunochemical reactivity of patient sera with phage‐expressed proteins showed enrichment on the number of immunogenic phage clones in the biopanning process and also confirmed that antibodies were present in patient sera but not in normal sera. Antibodies to five phage‐expressed proteins were measured by enzyme‐linked immunosorbent assay (ELISA) to validate the concept that combinations have greater predictive value than any single antibody alone. Logistic regression analysis showed that combined measurements of five antibodies was more predictive of disease than any single antibody alone, underscoring the importance of identifying multiple potential markers. The resulting antibody profiling is a feasible diagnostic strategy for NSCLC. An inventory of corresponding proteins may have significant relevance to tumor biology, novel drug development, and immunotherapies.
Functional and topological characterization of protein interaction networks
Authors: Yook Soon‐Hyung , Oltvai Zoltán N. , Barabási Albert‐László
Published: March 2004

The elucidation of the cell's large‐scale organization is a primary challenge for post‐genomic biology, and understanding the structure of protein interaction networks offers an important starting point for such studies. We compare four available databases that approximate the protein interaction network of the yeast, Saccharomyces cerevisiae, aiming to uncover the network's generic large‐scale properties and the impact of the proteins' function and cellular localization on the network topology. We show how each database supports a scale‐free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong correlations between the network's structure and the functional role and subcellular localization of its protein constituents, concluding that most functional and/or localization classes appear as relatively segregated subnetworks of the full protein interaction network. The uncovered systematic differences between the four protein interaction databases reflect their relative coverage for different functional and localization classes and provide a guide for their utility in various bioinformatics studies.
Proteomic analysis of the human pathogen Trypanosoma cruzi
Authors: Paba Jaime , Santana Jaime M. , Teixeira Antonio R. L. , Fontes Wagner , Sousa Marcelo V. , Ricart Carlos A. O.
Published: March 2004

Trypanosoma cruzi, the protozoan that causes Chagas disease, possesses a complex life cycle involving different developmental stages. Experimental conditions for two‐dimensional electrophoresis (2‐DE) analysis of T. cruzi trypomastigote, amastigote and epimastigote proteomes were optimized. Comparative proteome analysis of the cell‐cycle stages were carried out, revealing that few proteins included in the 2‐DE maps displayed significant differential expression among the three developmental forms of the parasite. In order to identify landmark proteins, spots from the trypomastigote 2‐DE map were subjected to matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry peptide mass fingerprinting, resulting in 26 identifications that corresponded to 19 different proteins. Among the identified polypeptides, there were heat shock proteins (HSP; chaperones, HSP 60, HSP 70 and HSP 90), elongation factors, glycolytic pathway enzymes (enolase, pyruvate kinase and 2,3 bisphosphoglycerate mutase) and structural proteins (KMP 11, tubulin and paraflagellar rod components). The relative expression of the identified proteins in the 2‐DE maps of the T. cruzi developmental stages is also presented.
Quantitative profiling of LNCaP prostate cancer cells using isotope‐coded affinity tags and mass spectrometry
Authors: Meehan Katie L. , Sadar Marianne D.
Published: March 2004

Androgens are involved in the pathogenesis of diseases including adenocarcinoma of the prostate. These hormones are important for growth, maintenance, and integrity of structure and function of the prostate. Androgen‐deprivation is currently the only effective systemic therapy for prostate cancer but the effects of androgens on the proteome are still poorly described. Here we quantitatively profile changes in the proteome of LNCaP human prostate cancer cells in response to androgen using the newly developed isotope‐coded affinity tag (ICAT) labeling and two‐dimensional liquid chromatography‐tandem mass spectroscopy (2‐D LC‐MS/MS). ICAT enables the concurrent identification and comparative quantitative analysis of proteins present in various biological samples including human cell and tissue extracts. Quantification and identification of 139 proteins in complex protein mixtures obtained from androgen‐stimulated and unstimulated LNCaP cells were achieved. Changes in levels of 77 proteins in response to androgens were detected. Some of these proteins have been previously reported to be regulated by androgens and include spermine synthase, fatty acid synthase and calreticulin precursor. A large number of proteins that have not been previously reported to be expressed in prostate cells were also quantitatively identified. Examples of these include members of the dual specificity protein phosphatase subfamily, “similar” to hypothetical protein DKFZp434B0328.1, “similar” to 14‐3‐3 protein zeta and “similar” to hypothetical protein 458, components of the actin cytoskeleton and a range of unknown/uncharacterized proteins. This catalogue of proteins provides an overview of the proteome of prostate cancer cells and the global changes that occur in response to androgens.
Improving large‐scale proteomics by clustering of mass spectrometry data
Authors: Beer Ilan , Barnea Eilon , Ziv Tamar , Admon Arie
Published: March 2004

Tandem mass spectrometry (MS/MS), coupled with liquid chromatography (LC), is a powerful tool for the analysis and comparison of complex protein and peptide mixtures. However, the extremely large amounts of data that result from the process are very complex and difficult to analyze. We show how the clustering of similar spectra from multiple LC‐MS/MS runs can help in data management and improve the analysis of complex peptide mixtures. The major effect of spectrum clustering is the reduction of the huge amounts of data to a manageable size. As a result, analysis time is shorter and more data can be stored for further analysis. Furthermore, spectrum quality improvement allows the identification of more peptides with greater confidence, the comparison of complex peptide mixtures is facilitated, and the entire proteomics project is presented in concise form. Pep‐Miner is an advanced software tool that implements these clustering‐based applications. It proved useful in several comparative proteomics projects involving lung cancer cells and various other cell types. In one of these projects, Pep‐Miner reduced 517 000 spectra to 20 900 clusters and identified 2518 peptides derived from 830 proteins. Clustering and identification lasted less than two hours on an IBM Thinkpad T23 computer (laptop). Pep‐Miner's unique properties make it a very useful tool for large‐scale shotgun proteomics projects.
Characterization of the human urinary proteome: A method for high‐resolution display of urinary proteins on two‐dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots
Authors: Pieper Rembert , Gatlin Christine L. , McGrath Andrew M. , Makusky Anthony J. , Mondal Madhu , Seonarain Michael , Field Erin , Schatz Courtney R. , Estock Marla A. , Ahmed Nasir , Anderson Norman G. , Steiner Sandra
Published: March 2004

The abundance profile of the human urinary proteome is known to change as a result of diseases or drug toxicities, particularly of those affecting the kidney and the urogenital tract. A consequence of such insults is the ability to identify proteins in urine, which may be useful as quantitative biomarkers. To succeed in discovering them, reproducible urine sample preparation methods and good protein resolution in two‐dimensional electrophoresis (2‐DE) gels for parallel semiquantitative protein measurements are desirable. Here, we describe a protein fractionation strategy enriching proteins of molecular masses (Mr) lower than 30 kDa in a fraction separate from larger proteins. The fraction containing proteins with Mrs higher than 30 kDa was subsequently subjected to immunoaffinity subtraction chromatography removing most of the highly abundant albumin and immunoglobulin G. Following 2‐DE display, superior protein spot resolution was observed. Subsequent high‐throughput mass spectrometry analysis of ca. 1400 distinct spots using matrix‐assisted laser desorption/ionization‐time of flight peptide mass fingerprinting and liquid chromatography‐electrospray ionization tandem mass spectrometry lead to the successful identification of 30% of the proteins. As expected from high levels of post‐translational modifications in most urinary proteins and the presence of proteolytic products, ca. 420 identified spots collapsed into 150 unique protein annotations. Only a third of the proteins identified in this study are described as classical plasma proteins in circulation, which are known to be relatively abundant in urine despite their retention to a large extent in the glomerular blood filtration process. As a proof of principle that our urinary proteome display effort holds promise for biomarker discovery, proteins isolated from the urine of a renal cell carcinoma patient were profiled prior to and after nephrectomy. Particularly, the decrease in abundance of the kininogen 2‐DE gel spot train in urine after surgery was striking.
A combination of proteomics, principal component analysis and transcriptomics is a powerful tool for the identification of biomarkers for macrophage maturation in the U937 cell line
Authors: Verhoeckx Kitty C. M. , Bijlsma Sabina , de Groene Els M. , Witkamp Renger F. , van der Greef Jan , Rodenburg Richard J. T.
Published: March 2004

The monocyte‐like human histiocytic lymphoma cell line U937 can be induced by phorbol 12‐myristate 13‐acetate (PMA) to undergo differentiation into a macrophage‐like phenotype. We have used two‐dimensional gel electrophoresis (2‐DE), oligonucleotide microarrays and principal component analysis (PCA) to characterize the U937 cell line as a model system for the differentiation of monocytes into macrophages. A total of 226 differentially expressed proteins were found, of which 41 were selected by PCA for identification using matrix‐assisted laser desorption/ionization tandem mass spectrometry. Based on the PCA results, three marker proteins were selected for confirmation of differential expression using Western blot and quantitative real time‐PCR. The selected marker proteins were: gamma interferon inducible lysosomal thiol reductase, cathepsin D and adipocyte‐fatty acid binding protein. All three proved to be good differentiation markers for macrophage maturation of U937 cells as well as peripheral blood‐derived macrophages. The transcriptomics data revealed a large number of additional putative differentiation markers in U937 macrophages, many of which are known to be expressed in peripheral blood‐derived macrophages. These include osteospontin, matrix metalloproteinase 9, and HC‐gp39. Our results show that the characteristics of U937 macrophages resemble those of inflammatory (exudate) macrophages, exemplified by the down‐regulation of 5' nucleotidase and the up‐regulation of leucine aminopeptidase mRNAs. In conclusion, using the powerful combination of transcriptomics, 2‐DE and PCA, our results show that U937 cells differentiated by PMA treatment are an excellent model system for monocyte derived macrophage generation from blood.
Quantification of C‐reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C‐labeled peptide standards
Authors: Kuhn Eric , Wu Jiang , Karl Johann , Liao Hua , Zolg Werner , Guild Brad
Published: March 2004

A general method for the quantification of proteins in human serum was developed using mass spectrometry (MS) and stable isotope‐labeled synthetic peptides as internal standards. Using this approach, C‐reactive protein (CRP), a diagnostic marker of rheumatoid arthritis (RA), was detected in serum samples taken from patients with either erosive or nonerosive RA and compared to healthy individuals. Small volumes of serum samples were enriched for low‐abundance proteins through the selective removal of human serum albumin (HSA), immunoglobulin G (IgG), and haptoglobin. After depletion of abundant proteins, the complexity of the protein mixture was further simplified using size exclusion chromatography (SEC) to fractionate denatured proteins into discrete molecular weight ranges. Fractions of interest containing CRP, Mr = 25 000, were pooled, digested with trypsin, and then fixed quantities of the synthetic peptides were added to the mixture. The mixture of tryptic peptides was subsequently analyzed by nanoflow chromatography‐tandem MS (nanoLC‐MS/MS) using multiple‐reaction monitoring (MRM) on a triple quadrupole mass spectrometer (TQ‐MS). The ratio of transition ions derived from the endogenous and isotope‐labeled peptides provided a quantitative measure of CRP in the original samples as assessed by independent measurement of CRP in the same patient samples using an immunoassay. The use of isotope‐labeled synthetic peptides and MRM is a powerful analytical method for the prescreening of candidate protein biomarkers in human serum prior to antibody and immunoassay development.
Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry
Authors: Chertov Oleg , Biragyn Arya , Kwak Larry W. , Simpson John T. , Boronina Tatiana , Hoang Van M. , Prieto DaRue A. , Conrads Thomas P. , Veenstra Timothy D. , Fisher Robert J.
Published: March 2004

A method to extract peptides and low molecular weight proteins from serum under denaturing conditions using acetonitrile containing 0.1% trifluoroacetic acid has been developed. The extraction procedure precipitates large, abundant proteins to simplify subsequent mass spectral analysis. This sample preparation method provides an efficient way to extract serum peptides, enabling them to be compared and identified using different mass spectrometry approaches. Surface‐enhanced laser desorption/ionization‐time of flight mass spectrometry analysis of mouse blood serum samples prepared by this method allowed detection of two markers which were significantly reduced in mice with B cell lymphoma tumor. One of these markers has been identified as apolipoprotein A‐II.
Contribution of the antibodies response induced by a low virulent Candida albicans strain in protection against systemic candidiasis
Authors: Fernández‐Arenas Elena , Molero Gloria , Nombela César , Diez‐Orejas Rosalía , Gil Concha
Published: March 2004

A low virulent Candida albicans mutant, CNC13, deleted in the Mitogen Activated Protein (MAP) kynase HOG1 was used to immunize BALB/c mice. Hog1p is essential for the oxidative stress and hyperosmolarity responses. Several doses and immunization procedures were employed. The protection capacity of the different sera generated was analyzed in a murine model of systemic candidiasis. Using a proteomic approach (two‐dimensional gel electrophoresis followed by Western blotting), we were able to distinguish two categories of serum: protective and nonprotective, which showed different titres of total Immunoglobulins (Igs) and IgG2a (analyzed by enzyme‐linked immunosorbent assay). The levels of Igs and IgG2a in protective sera were significantly higher compared to nonprotective sera. The pattern of a “nonprotective” profile was composed of enolase (Eno1p), transketolase, heat shock protein and methionine synthase. Only antibodies against enolase are the IgG2a isotype. The pattern of a “protective” sera, on the other hand, was composed of antibodies against the following antigens: several isoforms of Eno1p, pyruvate decarboxylase, pyruvate kynase, a protein of the 40S ribosomal subunit, triosephosphate isomerase, DL‐glycerol phosphatase and fructose‐bisphosphate aldolase. All these antibodies are the IgG2a isotype. The proteins described in the protective sera might be useful for future vaccine development.
Loss of BMP2, Smad8, and Smad4 expression in prostate cancer progression
Authors: Horvath Lisa G. , Henshall Susan M. , Kench James G. , Turner Jennifer J. , Golovsky David , Brenner Phillip C. , O'Neill Gordon F. , Kooner Raji , Stricker Phillip D. , Grygiel John J. , Sutherland Robert L.
Published: March 2004

BACKGROUND

The role of the bone morphogenetic protein (BMP) pathway in prostate cancer (PC) is unclear. This study aimed to characterize aspects of the BMP pathway in PC by assessing BMP2, Smad8, and Smad4 expression in normal, hyperplastic, and malignant prostate tissue, and to correlate findings with progression to PC.

METHODS

Radical prostatectomy (RP) specimens from 74 patients with clinically localized PC (median follow‐up 51 months, range 15–152), 44 benign prostatic hypertrophy (BPH) lesions, and 4 normal prostates (NPs) were assessed for BMP2, Smad8, and Smad4 expression using immunohistochemistry.

RESULTS

Both BMP2 (P < 0.001) and nuclear Smad4 (P < 0.0001) expression were significantly decreased in PC compared to benign prostate tissue. Nuclear Smad8 was present in normal/benign prostate tissue but absent in PC and adjacent hyperplasia. Furthermore, loss of BMP2 (P < 0.001) and decreased nuclear Smad4 (P = 0.05) expression correlated with increasing Gleason score.

CONCLUSIONS

These data suggest that decreased BMP2, nuclear smad8 and nuclear Smad4 expression are associated with the progression to PC, and in particular loss of BMP2 and Smad4 are related to progression to a more aggressive phenotype. © 2004 Wiley‐Liss, Inc.
The specific role of isoflavones in reducing prostate cancer risk
Authors: Kumar Nagi B. , Cantor Alan , Allen Kathy , Riccardi Diane , Besterman‐Dahan Karen , Seigne John , Helal Mohamad , Salup Raoul , Pow‐Sang Julio
Published: March 2004

AIMS

To evaluate the effectiveness of supplementing a group of early stage prostate cancer patients, with 60 mg of soy isoflavones in producing a change in hormonal and proliferative risk parameters that are implicated in prostate cancer promotion.

METHODS

Seventy six eligible prostate cancer patients with a Gleason score of 6 or below, between ages 50 and 80 were admitted and supplemented with soy isoflavones or placebo for a 12 week period and changes in PSA and steroid hormones were analyzed at baseline and post intervention.

RESULTS

Fifty‐nine patients completed the 12‐week intervention. Serum free testosterone was reduced or showed no change in 61% of subjects in the isoflavone group compared to 33% in the placebo group. Serum total PSA decreased or was unchanged in 69% of the subjects in the isoflavone treated group compared to 55% in the placebo group. However, we did not see an increase in SHBG levels. Nineteen percent of subjects receiving soy isoflavones reduced total PSA by two points or more during the intervention period.

CONCLUSIONS

These data suggest that supplementing early stage prostate cancer patients with soy isoflavones, even in a study of short duration, altered surrogate markers of proliferation such as serum PSA and free testosterone in a larger number of subjects in the isoflavone supplemented group than the group receiving placebo. The study establishes the need to explore further the effects of prolonged and consistent soy consumption, which could potentially delay onset of histologic disease in this patient population. © 2004 Wileey‐Liss, Inc.