bluuebunny/crossref_metadata_2025_split huggingface dataset:
Space–time patterns of co‐variation of biodiversity and primary production in phytoplankton guilds of coastal marine environments
Authors: Vadrucci Maria Rosaria , Vignes Fabio , Fiocca Annita , Basset Alberto , Santarpia Immacolata , Carrada Gian Carlo , Cabrini Marina , Umani Serena Fonda 
Published: October 2003

Abstract
The relevance of biodiversity to ecosystem processes is a major topic in ecology. Here, we analyse the relationship between biodiversity and productivity of the nano‐ and micro‐phytoplankton guilds in coastal marine ecosystems.
The patterns of variation of species richness, diversity and primary productivity (as 14C assimilation) were studied in two marine areas: a eutrophic–mesotrophic area beside the River Po delta (northern Adriatic) and an oligotrophic area around the Salento peninsula (southern Adriatic–Ionian). The study was carried out at 23 sites in the northern area and at 45 sites in the southern area. Sites were arranged on expected spatial and temporal gradients of primary productivity variation, according to distance from the coast, optical depths and seasonal period.
167 taxa were identified in the northern area and 153 taxa in the southern area. In both areas, the taxonomic composition of the nano‐ and micro‐phytoplankton guilds exhibited greater temporal than spatial variation. The latter was much higher in the southern area than in the northern area (average dissimilarity between stations being 70.7±0.8% and 44.7±4.2% respectively).
Primary productivity varied in space and time on the gradients considered. Phytoplankton species richness and diversity exhibited significant patterns of variation in space and time; overall, these were inversely related to the primary productivity patterns in the northern area, whereas they were directly related in the southern area.
The small individual size and the high turnover rate of phytoplankton are likely to underlie the observed relationships, which emphasized a threshold response to nutrient enrichment in agreement with the ‘paradox of enrichment’. Under resource enrichment conditions, the high turnover of producers leads to hierarchical partitioning of the available resources with an increasing dominance of a few species. Therefore, the relationship observed here seems likely to be explained by the complementarity hypothesis.
Copyright © 2003 John Wiley & Sons, Ltd.
The determination of ecological status in shallow lakes — a tested system (ECOFRAME) for implementation of the European Water Framework Directive
Authors: Moss Brian , Stephen Deborah , Alvarez Cristina , Becares Eloy , Bund Wouter Van De , Collings S.E. , Donk Ellen Van , Eyto Elvira De , Feldmann Tõnnu , Fernández‐Aláez Camino , Fernández‐Aláez Margarita , Franken Rob J.M. , García‐Criado Francisco , Gross Elisabeth M. , Gyllström Mikael , Hansson Lars‐Anders , Irvine Kenneth , Järvalt Ain , Jensen Jens‐Peder , Jeppesen Erik , Kairesalo Timo , Kornijów Ryszard , Krause Teet , Künnap Helen , Laas Alo , Lill Evi , Lorens Bogdan , Luup Helen , Rosa Miracle Maria , Nõges Peeter , Nõges Tiina , Nykänen Mirva , Ott Ingmar , Peczula Wojciech , Peeters Edwin T.H.M. , Phillips Geoff , Romo Susanna , Russell Victoria , Salujõe Jaana , Scheffer Marten , Siewertsen Klaus , Smal Halina , Tesch Claudia , Timm Henn , Tuvikene Lea , Tonno Ilmar , Virro Taavi , Vicente Eduardo , Wilson David 
Published: October 2003

Abstract
The European Water Framework Directive requires the determination of ecological status in European fresh and saline waters. This is to be through the establishment of a typology of surface water bodies, the determination of reference (high status) conditions in each element (ecotype) of the typology and of lower grades of status (good, moderate, poor and bad) for each ecotype. It then requires classification of the status of the water bodies and their restoration to at least ‘good status’ in a specified period.
Though there are many methods for assessing water quality, none has the scope of that defined in the Directive. The provisions of the Directive require a wide range of variables to be measured and give only general guidance as to how systems of classification should be established. This raises issues of comparability across States and of the costs of making the determinations.
Using expert workshops and subsequent field testing, a practicable pan‐European typology and classification system has been developed for shallow lakes, which can easily be extended to all lakes. It is parsimonious in its choice of determinands, but based on current limnological understanding and therefore as cost‐effective as possible.
A core typology is described, which can be expanded easily in particular States to meet local conditions. The core includes 48 ecotypes across the entire European climate gradient and incorporates climate, lake area, geology of the catchment and conductivity.
The classification system is founded on a liberal interpretation of Annexes in the Directive and uses variables that are inexpensive to measure and ecologically relevant. The need for taxonomic expertise is minimized.
The scheme has been through eight iterations, two of which were tested in the field on tranches of 66 lakes. The final version, Version 8, is offered for operational testing and further refinement by statutory authorities.
Copyright © 2003 John Wiley & Sons, Ltd.
Ductal lavage in patients undergoing mastectomy for mammary carcinoma
Authors: Brogi Edi , Robson Mark , Panageas Katherine S. , Casadio Chiara , Ljung Britt‐Marie , Montgomery Leslie 
Published: October 2003

AbstractBACKGROUNDDuctal lavage (DL) is a new method for the sampling of breast epithelium. Data regarding its sensitivity in the detection of epithelial abnormalities, including carcinoma in situ (CIS), remains limited.METHODSDL was performed in the affected breasts of 26 women undergoing mastectomy for mammary carcinoma and in the clinically normal breast of 4 additional women undergoing risk‐reducing mastectomy. After surgery, dye was injected through the microcatheter used for DL. Three cytopathologists independently reviewed all DL slides and the data reflect consensus by at least two reviewers. Interobserver agreement was assessed. The findings in DL samples were correlated with the features of CIS in the mastectomy specimens.RESULTSFour (14%) of 29 DL samples satisfactory for evaluation showed marked atypia, 10 (34%) showed mild atypia, and 15 (52%) were benign. No DL sample was clearly malignant. Interobserver agreement was good (average kappa = 0.52). Of the DL samples satisfactory for evaluation, 27 had been obtained from 24 breasts containing CIS, which included 18 ductal CIS (DCIS), 3 lobular CIS (LCIS), 2 DCIS and LCIS, and 1 solid CIS with mixed ductal and lobular features. Invasive carcinoma was present in 20 samples. Two DL samples from breasts with extensive LCIS showed mild atypia and injected dye was identified in ducts and lobules involved by LCIS.CONCLUSIONSDL had low sensitivity for CIS in breasts that also contained invasive carcinoma. The use of DL remains investigational, and close follow‐up should be continued for all patients undergoing DL, including those with benign diagnoses. Cancer 2003. © 2003 American Cancer Society.
Lifetime recreational exercise activity and risk of breast carcinoma in situ
Authors: Patel Alpa V. , Press Michael F. , Meeske Kathleen , Calle Eugenia E. , Bernstein Leslie 
Published: October 2003

AbstractBACKGROUNDThe incidence rates of breast carcinoma in situ (BCIS) have increased dramatically over the past two decades, primarily because of increased mammography screening. Ductal carcinoma in situ, which accounts for approximately 85% of BCIS and 10–20% of all breast carcinomas, is generally recognized as the final step in the progression to invasive disease. To the authors' knowledge, few studies have been conducted to date to evaluate BCIS risk factors. Because of its potential effects on circulating sex hormones, physical activity has been proposed as a modifiable risk factor for invasive breast carcinoma. However, the relation to BCIS risk is poorly understood.METHODSThe authors analyzed data from a population‐based case–control study conducted in Los Angeles County. Personal interviews were conducted with 567 white and black women (age range, 35–64 years) who had been newly diagnosed with BCIS between March 1, 1995 and May 31, 1998 and with 1026 control subjects, of whom 616 were screened within 2 years of identification.RESULTSAfter excluding unscreened control subjects (n = 410) and adjusting for potential confounding factors, the risk of BCIS was approximately 35% lower among women with any exercise activity compared with inactive women, although no significant trend was observed. The association between exercise activity and the risk of BCIS was modified by a family history of breast carcinoma. No reduction in risk was observed among women reporting a first‐degree family history of breast carcinoma (homogeneity of trends P value = 0.02).CONCLUSIONSThe findings of the current study suggest that exercise activity may modify the risk of BCIS, particularly among women without a family history of breast carcinoma. Cancer 2003. © 2003 American Cancer Society.
Revision of the International Neuroblastoma Pathology Classification
Authors: Peuchmaur Michel , d'Amore Emanuele S. G. , Joshi Vijay V. , Hata Jun‐ichi , Roald Borghild , Dehner Louis P. , Gerbing Robert B. , Stram Daniel O. , Lukens John N. , Matthay Katherine K. , Shimada Hiroyuki 
Published: October 2003

AbstractBACKGROUNDGanglioneuroblastoma, nodular (GNBn) comprises one of the categories of peripheral neuroblastic tumors. All tumors in this category, according to the original International Neuroblastoma Pathology Classification, are classified into an unfavorable histology group. Subsequently, it has been reported that GNBn can be divided into two prognostic subsets, a favorable subset (FS) and an unfavorable subset (US).METHODSHistology slides from 70 patients who were enrolled in Children's Cancer Group studies 3881 and 3891 and who had a diagnosis of GNBn were reviewed jointly by the members of International Neuroblastoma Pathology Committee (INPC): 1) to confirm the diagnosis of GNBn, 2) to identify the FS and US by applying the same age‐linked criteria that were used to distinguish the favorable histology group and unfavorable histology group in conventional neuroblastoma tumors from the neuroblastomatous component of GNBn tumors, and 3) to verify the significant prognostic difference between these two subsets. The patients had been used in a previous study, and survival data for the patients were updated since the time of their last report.RESULTSThe review clarified and illustrated morphologic characteristics of classical GNBn and it variants. The diagnosis of GNBn was confirmed in 67 of 70 patients. There were 22 patients with GNBn in the FS and 45 patients with GNBn in the US. The estimated survival differences between the FS and US patients with GNBn were statistically significant (8‐year event free survival rate: 86.1% vs. 32.2%; P = 0.0003; overall survival rate: 90.5% vs. 33.2%; P = 0.0003).CONCLUSIONSThis study confirmed the recently defined prognostic subsets of GNBn. The INPC proposes to modify the International Neuroblastoma Pathology Classification by distinguishing the FS and the US among patients with GNBn tumors. Cancer 2003. © 2003 American Cancer Society.
Outcome in 34 patients with juvenile‐onset mycosis fungoides
Authors: Wain E. Mary , Orchard Guy E. , Whittaker Sean J. , Spittle M.Sc. Margaret F. , Russell‐Jones Robin 
Published: October 2003

AbstractBACKGROUNDMycosis fungoides (MF) is predominantly a disease of older patients, but occasionally occurs in children. The aims of the current study were to describe the clinical presentation, pathologic features, and disease progression (DP) in patients who developed MF before age 16 years.METHODSA retrospective study was performed. Patients with juvenile‐onset MF were identified from our databases. Clinical features were determined from the medical records and patient interviews. Histologic, immunohistochemical, and T‐cell receptor (TCR) gene analysis was performed.RESULTSThirty‐four patients were identified: 50% had Stage IA disease, 47% had Stage IB disease, and 3% had Stage IIA disease. The male‐to‐female ratio was 2:1. Clinical features included hypopigmented lesions (24%), poikiloderma (26%), pilotropic disease (9%), and disease associated with lymphomatoid papulosis (18%). Twenty‐eight patients had diagnostic histology, and six patients were included on the basis of compatible histology and a TCR clone in lesional skin. A cytotoxic immunophenotype was observed in 38%, including 71% of patients with hypopigmented lesions. Overall disease‐specific survival (DSS) rates at 5 and 10 years were 95% and 93%, respectively. DP rates were 5% at 5 years and 29% at 10 years. Subgroup analysis demonstrated improved DSS and reduced DP in patients with Stage IA disease, those with hypopigmented or poikilodermatous lesions, and those with associated lymphomatoid papulosis.CONCLUSIONSThe prognosis for juvenile‐onset MF is similar to that of adult‐onset disease. There was an overrepresentation of a cytotoxic phenotype, which was most marked in hypopigmented variants. Widespread cutaneous disease (Stage IB) indicated a less favorable outcome. Cancer 2003. © 2003 American Cancer Society.
Clear cell ependymoma: A clinicopathologic and radiographic analysis of 10 patients
Authors: Fouladi Maryam , Helton Kathleen , Dalton James , Gilger Elizabeth , Gajjar Amar , Merchant Thomas , Kun Larry , Newsham Irene , Burger Peter , Fuller Christine 
Published: October 2003

AbstractBACKGROUNDClear cell ependymoma (CCE) is an uncommon central nervous system tumor with a predilection for the supratentorial region in children. Histologically, it may mimic oligodendroglioma, central neurocytoma, hemangioblastoma, and renal cell carcinoma.METHODSThe authors reviewed the clinical, radiographic, and pathologic features, therapy, and outcome in 10 children with CCE who were treated at St. Jude Children's Research Hospital (1984–2003). Fluorescence in situ hybridization (FISH) was performed using 1p/1q, 19p/19q, CEP18/DAL1, and bcr/NF2 probe pairs.RESULTSThe median patient age at diagnosis was 7.5 years (range, 1–19 years). Tumors occurred supratentorially in 9 of 10 patients. All tumors had rounded nuclei with surrounding, clear halos and at least focal perivascular pseudorosettes. Seven tumors had anaplastic features. No deletions involving 1p, 19q, or NF2 were detected. The tumors from 5 of 7 patients, all with anaplasia, had losses of both CEP18 and DAL‐1. Radiographically, all tumors were enhanced, and 9 tumors had associated cysts with enhancing walls. Seven patients underwent gross total resection, which was near total in one patient and subtotal in two patients. Five patients received immediate postoperative local radiotherapy. Three patients were diagnosed initially with pilocytic astrocytoma (one patient) and oligodendroglioma (two patients) and were observed. The progression‐free survival and overall survival rates at 5 years were 34% ± 20% and 75% ± 19%, respectively. The median follow‐up was 37 months (range, 5–239 months). Five patients developed local recurrence within a median of 9 months after diagnosis. Two patients developed extracranial soft tissue and lymph node metastases.CONCLUSIONSCCEs were found to have a predilection for extraneural metastases and early recurrence and demonstrate characteristic radiographic features, anaplastic histologic features, and chromosome 18 losses. The authors recommend resection followed by local radiotherapy as the treatment of choice in children. Cancer 2003. © 2003 American Cancer Society.
The role of late/slow replication of the FRA16D in common fragile site induction
Authors: Palakodeti Aparna , Han Yu , Jiang Yanwen , Le Beau Michelle M. 
Published: October 2003

AbstractThe FRA16D, at 16q23, spans the WWOX gene and is one of the most highly expressed common fragile sites observed when DNA replication is perturbed by aphidicolin. Several lines of evidence suggest that fragile sites are regions of DNA that are unusually sensitive to interference during replication. We have determined that the FRA16D alleles replicate in a synchronous fashion and that replication of these sequences occurs primarily in late S phase extending into G2 phase. Exposure to aphidicolin, an inhibitor of DNA polymerase α, results in a modest increase in cells with replication of FRA16D sequences in early S phase. This may represent initiation of replication in early S phase coupled with slow replication progression, or, alternatively, these cells may have passed through mitosis, entered the G1‐S phase of the next cell cycle, and initiated replication/repair. Our results support a model in which common fragile sites are sequences that may initiate replication in early‐mid S phase but are slow to complete replication, and the chromosomal breaks and gaps observed in metaphase cells result from unreplicated DNA. © 2003 Wiley‐Liss, Inc.
Frequent amplification and rearrangement of chromosomal bands 6p12‐p21 and 17p11.2 in osteosarcoma
Authors: Lau Ching C. , Harris Charles P. , Lu Xin‐Yan , Perlaky Laszlo , Gogineni Sheila , Chintagumpala Murali , Hicks John , Johnson Mark E. , Davino Nelson A. , Huvos Andrew G. , Meyers Paul A. , Healy John H. , Gorlick Richard , Rao Pulivarthi H. 
Published: October 2003

AbstractOsteosarcoma (OS) is a highly malignant bone neoplasm of children and young adults. It is characterized by chaotic karyotypes with complex marker chromosomes. We applied a combination of molecular cytogenetic techniques including comparative genomic hybridization (CGH), spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH) to decipher the chromosomal complexity in a panel of 25 tumors. Combined SKY and G‐banding analysis identified several novel recurrent breakpoint clusters and 9 nonrecurrent reciprocal translocations. CGH identified several recurrent chromosomal losses including 2q, 3p, 9, 10p, 12q, 13q, 14q, 15q, 16, 17p, and 18q, gains including Xp, Xq, 5q, 6p, 8q, 17p, and 20q, and high‐level chromosomal amplifications at Xp11.2, 1q21‐q22, 4p11, 4q12, 5p15, 6p12.1, 8q13, 8q23, 10q11, 10q22, 11q13, 11q23, 12q13‐q14, 13q21‐q34, 16q22, 17p11.2, 17q21‐q22, 18q22, 20p11.2, and 20q12. Frequent amplification and rearrangement involving chromosomal bands at 6p12‐p21 and 17p11.2 were found in 28% and 32% of cases, respectively. In an attempt to identify the genes involved in these amplicons, we used three nonoverlapping BAC clones contained within each amplicon as probes for FISH analysis, leading to a more detailed characterization and quantification of the 6p and 17p amplicons. © 2004 Wiley‐Liss, Inc.
Novel regions of amplification on 8q distinct from the MYC locus and frequently altered in oral dysplasia and cancer
Authors: Garnis Cathie , Coe Bradley P. , Ishkanian Adrian , Zhang Lewei , Rosin Miriam P. , Lam Wan L. 
Published: October 2003

AbstractGenetic studies aimed at identifying key alterations in oral cancers have focused on analysis of tumors, with few such studies using early oral premalignant lesions (OPLs) because of limitations in both sample availability and size. In this study, we used a randomly amplified polymorphic DNA (RAPD)‐PCR approach to fingerprint DNA from microdissected normal and dysplastic cells and identified two recurrent genetic alterations on the long arm of chromosome 8 in OPLs, one mapping to 8q22 and the other to 8q24 near the MYC locus. We constructed a high‐resolution bacterial artificial chromosome (BAC) comparative genomic hybridization array consisting of 166 overlapping BAC clones that spans about 52 Mbp, from 8q21 to 8q24. Hybridization of DNA from microdissected oral tumors to the array revealed alteration at 8q24, with amplification of the BAC containing MYC. Strikingly, at least two other novel regions of amplification at 8q22 were identified. Microsatellite analysis of 93 oral dysplasias and tumors confirmed the presence of one of the alterations at 8q22. Loss of heterozygosity (LOH) at D8S1830, mapping within one of the regions of amplification, was observed in high frequency in both OPLs and tumors. Of the 37 cases with LOH at D8S1830, 23 (62%) showed retention at D8S1793, which maps 1.6 Mbp centromeric to MYC. This is further support for the alteration at 8q22 being distinct from MYC. These data raise the possibility of additional oncogenes on 8q near the MYC locus that are potentially involved in OPL disease progression. © 2003 Wiley‐Liss, Inc.
Contrasting in vivo and in vitro fates of glioblastoma cell subpopulations with amplified EGFR
Authors: Pandita Ajay , Aldape Kenneth D. , Zadeh Gelareh , Guha Abhijit , James C. David 
Published: October 2003

AbstractDespite the high incidence of EGFR amplification in patient glioblastoma multiforme (GBM) tissues, only a single GBM cell line, of the many described in the literature, is known to contain and maintain amplified EGFR. Because EGFR mutations in GBM manifest primarily, if not exclusively, in amplified form, it follows that the availability of cell lines with mutation of endogenous EGFR would also be in short supply. In fact, there are no GBM cell lines harboring the common EGFR mutants described in patient GBMs. These observations suggest that in vivo environments select for EGFR amplification, whereas in vitro environments, specifically cell cultures, select against this gene alteration. To contrast directly the fates of EGFR amplification in vivo and in vitro, as well as to examine potential relationships between EGFR amplification and mutation, we have established and maintained GBM explants as xenografts by serial passaging in nude mice. Analysis of EGFR copy number and EGFR mutation status in 11 patient tumors and their corresponding xenografts, as well as the monitoring of EGFR copy number during the establishment of a GBM cell line from a xenograft with amplified EGFR, indicated that selection for EGFR amplification is an in vivo phenomenon. Furthermore, our data indicated that EGFR mutation occurs only in tumors with EGFR amplification and showed that the selection of amplified mutant EGFR over amplified wild‐type EGFR as a xenograft occurred rapidly and completely during tumor propagation. © 2003 Wiley‐Liss, Inc.
A nonredundant multicolor bar code as a screening tool for rearrangements in neoplasia
Authors: Müller Stefan , Eder Verena , Wienberg Johannes 
Published: October 2003

AbstractA chromosome bar code describes the colored pattern of chromosome segments and is derived by multicolor fluorescence in situ hybridization (FISH) of defined molecular probes. Published approaches to the simultaneous differentiation of whole karyotypes with bar codes have not allowed the unequivocal identification of all chromosome segments because of color redundancy of the patterns from a multitude of identically colored segments. Here, we present a chromosome bar code approach in which the problem of color redundancy has been overcome. It allows the detailed description of translocations, including breakpoints as well as intrachromosomal rearrangements in the karyotype of tumor cells. The resolution of discernable bars was increased to 100 bars per haploid chromosome set by including human chromosome–specific probes and more well‐defined subregional probes such as chromosome arm‐ and segment‐specific probes. Technically, no limitation to further increase in the resolution of the pattern became apparent. The approach was validated by the analysis of four established tumor cell lines widely used as models in cell biology, revealing numerous inter‐ and intrachromosomal rearrangements. Chromosome bar coding as presented here may provide further useful information for the subregional assignment of chromosomal breakpoints in complex chromosome aberrations, as found in various neoplasms that cannot be obtained by chromosome painting or classical banding techniques alone. © 2003 Wiley‐Liss, Inc.