bluuebunny/crossref_metadata_2025 huggingface dataset:
A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity
Authors: Huang R. Stephanie , Duan Shiwei , Bleibel Wasim K. , Kistner Emily O. , Zhang Wei , Clark Tyson A. , Chen Tina X. , Schweitzer Anthony C. , Blume John E. , Cox Nancy J. , Dolan M. Eileen
Published: May 2007

Large interindividual variance has been observed in sensitivity to drugs. To comprehensively decipher the genetic contribution to these variations in drug susceptibility, we present a genome-wide model using human lymphoblastoid cell lines from the International HapMap consortium, of which extensive genotypic information is available, to identify genetic variants that contribute to chemotherapeutic agent-induced cytotoxicity. Our model integrated genotype, gene expression, and sensitivity of HapMap cell lines to drugs. Cell lines derived from 30 trios of European descent (Center d'Etude du Polymorphisme Humain population) and 30 trios of African descent (Yoruban population) were used. Cell growth inhibition at increasing concentrations of etoposide for 72 h was determined by using alamarBlue assay. Gene expression on 176 HapMap cell lines (87 Center d'Etude du Polymorphisme Humain population and 89 Yoruban population) was determined by using the Affymetrix GeneChip Human Exon 1.0ST Array. We evaluated associations between genotype and cytotoxicity, genotype and gene expression and correlated gene expression of the identified candidates with cytotoxicity. The analysis identified 63 genetic variants that contribute to etoposide-induced toxicity through their effect on gene expression. These include genes that may play a role in cancer (
AGPAT2
,
IL1B
, and
WNT5B
) and genes not yet known to be associated with sensitivity to etoposide. This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes induced by chemotherapeutic agents.
Boundary behavior of conformal deformations
Authors: Nieminen Tomi , Tossavainen Timo
Published: May 2007

We study conformal deformations of the Euclidean metric in the unit ball

B

n

\mathbb {B}^{n}

. We assume that the density associated with the deformation satisfies a Harnack inequality and an arbitrary volume growth condition on the isodiametric profile. We establish a Hausdorff (gauge) dimension estimate for the set

E
⊂
∂

B

n

E\subset \partial \mathbb {B}^{n}

where such a deformation mapping can “blow up”. We also prove a generalization of Gerasch’s theorem in our setting.
Identification ofArabidopsisCyclase-associated Protein 1 as the First Nucleotide Exchange Factor for Plant Actin
Authors: Chaudhry Faisal , Guérin Christophe , von Witsch Matthias , Blanchoin Laurent , Staiger Christopher J.
Published: May 2007

The actin cytoskeleton powers organelle movements, orchestrates responses to abiotic stresses, and generates an amazing array of cell shapes. Underpinning these diverse functions of the actin cytoskeleton are several dozen accessory proteins that coordinate actin filament dynamics and construct higher-order assemblies. Many actin-binding proteins from the plant kingdom have been characterized and their function is often surprisingly distinct from mammalian and fungal counterparts. The adenylyl cyclase-associated protein (CAP) has recently been shown to be an important regulator of actin dynamics in vivo and in vitro. The disruption of actin organization in cap mutant plants indicates defects in actin dynamics or the regulated assembly and disassembly of actin subunits into filaments. Current models for actin dynamics maintain that actin-depolymerizing factor (ADF)/cofilin removes ADP–actin subunits from filament ends and that profilin recharges these monomers with ATP by enhancing nucleotide exchange and delivery of subunits onto filament barbed ends. Plant profilins, however, lack the essential ability to stimulate nucleotide exchange on actin, suggesting that there might be a missing link yet to be discovered from plants. Here, we show that Arabidopsis thaliana CAP1 (AtCAP1) is an abundant cytoplasmic protein; it is present at a 1:3 M ratio with total actin in suspension cells. AtCAP1 has equivalent affinities for ADP– and ATP–monomeric actin (Kd∼ 1.3 μM). Binding of AtCAP1 to ATP–actin monomers inhibits polymerization, consistent with AtCAP1 being an actin sequestering protein. However, we demonstrate that AtCAP1 is the first plant protein to increase the rate of nucleotide exchange on actin. Even in the presence of ADF/cofilin, AtCAP1 can recharge actin monomers and presumably provide a polymerizable pool of subunits to profilin for addition onto filament ends. In turnover assays, plant profilin, ADF, and CAP act cooperatively to promote flux of subunits through actin filament barbed ends. Collectively, these results and our understanding of other actin-binding proteins implicate CAP1 as a central player in regulating the pool of unpolymerized ATP–actin.
Clustering microarray-derived gene lists through implicit literature relationships
Authors: Burkart Mark F. , Wren Jonathan D. , Herschkowitz Jason I. , Perou Charles M. , Garner Harold R.
Published: May 2007

Motivation: Microarrays rapidly generate large quantities of gene expression information, but interpreting such data within a biological context is still relatively complex and laborious. New methods that can identify functionally related genes via shared literature concepts will be useful in addressing these needs.

Results: We have developed a novel method that uses implicit literature relationships (concepts related via shared, intermediate concepts) to cluster related genes. Genes are evaluated for implicit connections within a network of biomedical objects (other genes, ontological concepts and diseases) that are connected via their co-occurrences in Medline titles and/or abstracts. On the basis of these implicit relationships, individual gene pairs are scored using a probability-based algorithm. Scores are generated for all pairwise combinations of genes, which are then clustered based on the scores. We applied this method to a test set composed of nine functional groups with known relationships. The method scored highly for all nine groups and significantly better than a benchmark co-occurrence-based method for six groups. We then applied this method to gene sets specific to two previously defined breast tumor subtypes. Analysis of the results recapitulated known biological relationships and identified novel pathway relationships unique to each tumor subtype. We demonstrate that this method provides a valuable new means of identifying and visualizing significantly related genes within gene lists via their implicit relationships in the literature.

Contact:  mark.burkart@utsouthwestern.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Occurrence of Rust Caused by Puccinia carthami on Snow Lotus in China
Authors: Zhao S. , Xie G.-L. , Li H. , Li C.
Published: May 2007

Snow lotus (Saussurea involucrata (Kar. & Kir.) Sch. Bip.) is an economically important medicinal herb increasingly grown in China in recent years. In August 2005, a rust disease on snow lotus plants commercially grown was found in the Tianshan mountain area of Xinjiang at 2,100 m above sea level. Disease incidence was approximately 15% of the plants observed in a commercial field in 2006. At the initial stage, tiny (1 to 2 mm long), orange brown pustules are formed on leaves. Later in the season, pustules turned chestnut brown to form bigger rust patches. Severely attacked leaves may die prematurely. During the growing season, rust pustules broke open to release reddish brown spores that cause secondary infection. The infected snow lotus plants were sampled, and the urediniospores and teliospores were observed for identification with a light microscope (4). Urediniospores were globose or broadly ellipsoid, 22 to 28 × 22 to 25 μm; teliospores were slightly or not constricted at the septum, 31.5 to 41.5 × 21.5 to 26.5 μm, wall was sienna to fulvous, occasionally chestnut colored, and pedicels were basal or oblique, verrucose, hyaline, and fragile. The pathogenicity test of the fungus was done by burying five leaves bearing telia around the roots of healthy safflower seedlings grown in a greenhouse under controlled conditions (25°C and 70% relative humidity) and healthy snow lotus seedlings grown under natural conditions with five replications. Symptoms were evaluated 60 days after inoculation. Similar rust symptoms were observed on both the snow lotus and safflower seedlings (1). The pycnidial and aecial stages of this autoecious rust were not observed in nature or the pathogenicity tests. The teliospores were reisolated and deposited at the Key Oasis Eco-Agriculture Laboratory of Xinjiang Production and Construction Group, Xinjiang and the Institute of Biotechnology, Zhejiang University. The causal organism of rust of snow lotus was identified as Puccinia carthami Corda on the basis of the morphology and pathogenicity test. To our knowledge, this is the first report of this rust on snow lotus (S. involucrata) (1–4).

References: (1) W. L. Bruckart. Plant Dis. 83:181, 1999. (2) M. L. Deadman et al. Plant Dis. 89:208, 2005. (3) S. J. Kolte. Diseases of annual edible oilseeds crops. In: Rapeseed-Mustard and Sesame Diseases. Vol. II. CRC Press, Boca Raton, FL, 1985. (4) G. F. Laundon. N. Z. J. Bot. 8:310, 1970.
Farm Management Effects on Rhizosphere Colonization by Native Populations of 2,4-Diacetylphloroglucinol-Producing Pseudomonas spp. and Their Contributions to Crop Health
Authors: Rotenberg Dorith , Joshi Raghavendra , Benitez Maria-Soledad , Chapin Laura Gutierrez , Camp Amara , Zumpetta Clara , Osborne Adam , Dick Warren A. , Gardener Brian B. McSpadden
Published: May 2007

Analyses of multiple field experiments indicated that the incidence and relative abundance of root-colonizing phlD+ Pseudomonas spp. were influenced by crop rotation, tillage, organic amendments, and chemical seed treatments in subtle but reproducible ways. In no-till corn plots, 2-year rotations with soybean resulted in plants with approximately twofold fewer phlD+ pseudomonads per gram of root, but 3-year rotations with oat and hay led to population increases of the same magnitude. Interestingly, tillage inverted these observed effects of cropping sequence in two consecutive growing seasons, indicating a complex but reproducible interaction between rotation and tillage on the rhizosphere abundance of 2,4-diacetlyphloroglucinol (DAPG) producers. Amending conventionally managed sweet corn plots with dairy manure compost improved plant health and also increased the incidence of root colonization when compared with nonamended plots. Soil pH was negatively correlated to rhizosphere abundance of phlD+ pseudomonads in no-till and nonamended soils, with the exception of the continuous corn treatments. Chemical seed treatments intended to control fungal pathogens and insect pests on corn also led to more abundant populations of phlD in different tilled soils. However, increased root disease severity generally was associated with elevated levels of root colonization by phlD+ pseudomonads in no-till plots. Interestingly, within a cropping sequence treatment, correlations between the relative abundance of phlD and crop stand or yield were generally positive on corn, and the strength of those correlations was greater in plots experiencing more root disease pressure. In contrast, such correlations were generally negative in soybean, a difference that may be partially explained by difference in application of N fertilizers and soil pH. Our findings indicate that farming practices can alter the relative abundance and incidence of phlD+ pseudomonads in the rhizosphere and that practices that reduce root disease severity (i.e., rotation, tillage, and chemical seed treatment) are not universally linked to increased root colonization by DAPG-producers.
Prevalence of avian influenza and host ecology
Authors: Garamszegi László Zsolt , Møller Anders Pape
Published: May 2007

Waterfowl and shorebirds are common reservoirs of the low pathogenic subtypes of avian influenza (LPAI), which are easily transmitted to poultry and become highly pathogenic. As the risk of virus transmission depends on the prevalence of LPAI in host-reservoir systems, there is an urgent need for understanding how host ecology, life history and behaviour can affect virus prevalence in the wild. To test for the most important ecological correlates of LPAI virus prevalence at the interspecific level, we applied a comparative analysis by using quantitative data on 30 bird species. We controlled for similarity among species due to common descent, differences in study effort and for covariance among ecological variables. We found that LPAI prevalence is a species-specific attribute and is a consequence of virus susceptibility, as it was negatively associated with the relative size of the bursa of Fabricius, an estimate of juvenile immune function. Species that migrate long distances have elevated prevalence of LPAI independent of phylogeny and other confounding factors. There was also a positive interspecific relationship between the frequency of surface feeding and virus prevalence, but this was sensitive to phylogenetic relatedness of species. Feeding in marine habitats is apparently associated with lower virus prevalence, but the effect of water salinity is likely to be indirect and affected by phylogeny. Our results imply that virus transmission via surface waters and frequent intra- and interspecific contacts during long migration are the major risk factors of avian influenza in the wild. However, the link between exploitation of surface waters and LPAI prevalence appears to be weaker than previously thought. This is the first interspecific study that provides statistical evidence that host ecology, immunity and phylogeny have important consequence for virus prevalence.
Grazing protozoa and the evolution of the
Escherichia coli
O157:H7 Shiga toxin-encoding prophage
Authors: Meltz Steinberg Karyn , Levin Bruce R
Published: May 2007

Humans play little role in the epidemiology of
Escherichia coli
O157:H7, a commensal bacterium of cattle. Why then does
E. coli
O157:H7 code for virulence determinants, like the Shiga toxins (Stxs), responsible for the morbidity and mortality of colonized humans? One possibility is that the virulence of these bacteria to humans is coincidental and these virulence factors evolved for and are maintained for other roles they play in the ecology of these bacteria. Here, we test the hypothesis that the carriage of the Stx-encoding prophage of
E. coli
O157:H7 increases the rate of survival of
E. coli
in the presence of grazing protozoa,
Tetrahymena pyriformis
. In the presence but not the absence of
Tetrahymena,
the carriage of the Stx-encoding prophage considerably augments the fitness of
E. coli
K-12 as well as clinical isolates of
E. coli
O157 by increasing the rate of survival of the bacteria in the food vacuoles of these ciliates. Grazing protozoa in the environment or natural host are likely to play a significant role in the ecology and maintenance of the Stx-encoding prophage of
E. coli
O157:H7 and may well contribute to the evolution of the virulence of these bacteria to colonize humans.
Determination of metastasis‐associated proteins in non‐small cell lung cancer by comparative proteomic analysis
Authors: Tian Tian , Hao Jia , Xu Anjian , Hao Juanting , Luo Chonglin , Liu Chuanjun , Huang Lingyun , Xiao Xueyuan , He Dacheng
Published: May 2007

The development of metastasis is the leading cause of death and an enormous therapeutic challenge in cases of non‐small cell lung cancer. To better understand the molecular mechanisms underlying the metastasis process and to discover novel potential clinical markers for non‐small cell lung cancer, comparative proteomic analysis of two non‐small cell lung cancer cell lines with different metastatic potentials, the non‐metastatic CL1‐0 and highly metastatic CL1‐5 cell lines, was carried out using two‐dimensional electrophoresis followed by matrix‐assisted laser desorption ionization–time of flight mass spectrometry and tandem mass spectrometry. Thirty‐three differentially expressed proteins were identified unambiguously, among which 16 proteins were significantly upregulated and 17 proteins were downregulated in highly metastatic CL1‐5 cells compared with non‐metastatic CL1‐0 cells. Subsequently, 8 of 33 identified proteins were selected for further validation at the mRNA level using real‐time quantitative polymerase chain reaction, and three identified proteins, S100A11, PGP 9.5 and HSP27, were confirmed by western blotting. The protein S100A11 displaying significant differential expression at both the protein and mRNA levels was further analyzed by immunohistochemical staining in 65 primary non‐small cell lung cancer tissues and 10 matched local positive lymph node specimens to explore its relationship with metastasis. The results indicated that the upregulation of S100A11 expression in non‐small cell lung cancer tissues was significantly associated with higher tumor–node–metastasis stage (P = 0.001) and positive lymph node status (P = 0.011), implying that S100A11 might be an important regulatory molecule in promoting invasion and metastasis of non‐small cell lung cancer. (Cancer Sci 2007; 98: 1265–1274)
Helminths and protozoa as an incidental finding in cytology specimens
Authors: LEARMONTH G. M. , MURRAY M. M.
Published: May 2007

This is a description of some helminths and protozoa found incidentally in routine cytology specimens submitted to this laboratory. Eight different organisms are described together with the case history for each patient. All the specimens were stained with Papanicolaou technique.
Fine needle aspiration cytology in a case of osteogenic sarcoma in Paget's disease
Authors: HAKKY M. , KOLBUSZ R. , REYES C. V. , CHINOY M. J.
Published: May 2007

A case of monostotic Paget's osteogenic sarcoma initially diagnosed by fine needle aspiration cytology is reported. The value of electron microscopy in this case is emphasized.
Burkitt's lymphoma: a pericardial presentation
Authors: GRAHAM S. J. , DUVAL‐ARNOULD B. , MERCADO T. C. , TREPEL J. B. , COTELINGAM J. D.
Published: May 2007

Described herein is a case of childhood Burkitt's lymphoma initially presenting as a pericardial effusion. A cytological diagnosis was made from a Wright's‐Giemsa stained cytospin preparation. Supporting diagnostic evidence was provided by immunological surface marker analysis and electron microscopy. To our knowledge, Burkitt's lymphoma has not hitherto been diagnosed initially from the morphology of cells in pericardial fluid.
A prospective study of human papillomavirus infection of the cervix
Authors: BYRNE M. A. , PARRY G. C. N. , MORSE A. , TAYLOR‐ROBINSON D. , MALCOLM A. D. B. , COLEMAN D. V.
Published: May 2007

In a prospective study 42 women, diagnosed as having low grade cervical intraepithelial neoplasia (CIN), made a total of 281 clinic visits over a 45 month period. At each visit, they were subjected to cytological and colposcopical examination and samples were taken for human papillomavirus (HPV) DNA hybridization studies and for the detection of non‐HPV infections. HPV types 16 and/or 18 were found in 25% of all the samples tested and these virus types were detected in five of six (83%) women whose lesions progressed compared to seven of 14 (50%) of those whose lesions regressed. The presence of HPV DNA was not a good prognostic indicator of progression since half of those whose disease regressed also harboured these viruses at some time. The recording of non‐HPV infections almost 10 times more often in the women whose disease regressed than in those whose disease progressed could probably be accounted for by the former having a larger number of follow‐up visits. Nevertheless, the significance of non‐HPV infections also remains unclear.
Audit of Diagnostic Accuracy of Fna Cytology Specimens Taken By the Histopathologist In A Symptomatic Breast Clinic
Authors: BROWN L. A. , COGHILL S. B. , POWIS S. A. J.
Published: May 2007

One thousand and two patients with palpable breast lumps have had fine needle aspiration at a surgical symptomatic breast clinic where the pathologist takes, stains and immediately reports the aspiration cytology smears. High levels of complete sensitivity (95.7%) and specificity (100%) have been maintained with a combined complete sensitivity for aspiration cytodiagnosis, mammography and clinical assessment of 99.7%. Significant reductions of unnecessary biopsies and out‐patient revisits have allowed major resource savings to be made. In view of the high degree of accuracy obtained by this approach to the investigation of palpable breast lesions, combined clinics with their benefits for the patient, both physical and psychological, should be encouraged.
A One Year Audit of Fine Needle Aspiration Cytology For the Pre‐Operative Diagnosis of Breast Disease
Authors: HITCHCOCK A. , HUNT C. M. , LOCKER A. , KOSLOWSKI J. , STRUDWICK S. , ELSTON C. W. , BLAMEY R. W. , ELLIS I. O.
Published: May 2007

In 1988, 985 patients presenting with breast disease, most with a palpable abnormality, were investigated by the triple approach (clinical examination, imaging and fine needle aspiration cytology [FNAC]). Using FNAC, 28% of patients were diagnosed as having carcinoma, 45% benign disease, 4% had suspicious cytology and 3% equivocal cytology. the remaining 20% had inadequate aspirates. Two false positive diagnoses of carcinoma were made (a false positive rate of 0.7%); one was a case of high grade non‐Hodgkin's lymphoma and the other a papillary lesion with epithelial atypia. the false negative rate was 6.4%. of these 49 patients, six had carcinoma‐in‐situ and 19 had low grade tumours. the absolute and complete sensitivities for the diagnosis of carcinoma in this series were 84.7% and 91.9% respectively and the absolute and complete specificities 99.7% and 98.3%, respectively. These figures compare favourably with those from other centres and confirm the efficacy of FNAC as part of the triple approach to the diagnosis of breast disease. the use of FNAC has resulted in a reduction in the numbers of Trucut and frozen section biopsies performed. Eighty three per cent of the patients with benign disease diagnosed by the triple approach have avoided excision biopsy, none of whom have subsequently been found to have carcinoma. Eighty patients with advanced breast carcinoma were spared operative intervention.
Can Flow Cytometry Reduce the Workload For Cervical Screening? the Results of A Series of 622 Specimens
Authors: TITLEY I. , TEE D. E. H. , DRIVER M. , DAVIES D. C. , ADAMS R. L.
Published: May 2007

A simple method permitting the flow cytometric examination of cervical specimens has been developed and an assessment made of the feasibility of relying on this method to screen women for cervical neoplasia. Examination of four flow cytometric parameters showed differences between morphologically normal and abnormal specimens and allowed identification of a proportion of the normal specimens. the system had a false negative rate of 8%. Our experience with cervical specimens has revealed a number of problems associated with their examination by flow cytometry and these are discussed.
Out‐Patient Peritoneal Lavage Cytology In the Detection of Residual Epithelial Ovarian Cancer
Authors: REDMAN C. W. E. , CHAPMAN S. E. , CHAN S. Y. , BUXTON E. J. , BLACKLEDGE G. , LUESLEY D. M.
Published: May 2007

Peritoneal lavage fluid cytology was performed in 87 out‐patients with histologically proven epithelial ovarian cancer undergoing primary management. A total of 246 peritoneal lavages were attempted, usually with temporary cannulae (n= 229). From these, 184 samples were obtained, of which 156 (85%) were suitable for cytological analysis. the sensitivity of peritoneal lavage fluid cytology in 67 patients with known residual disease was 57% whereas serum CA 125 levels were elevated in 58 (87%). Pre‐ and post‐treatment peritoneal lavage fluid cytology had prognostic value, but this was less than that of serum CA 125 measurements.
Diagnosis of Metastatic Pleomorphic Giant Cell Carcinoma of the Pancreas Using Fine Catheter Aspiration Cytology
Authors: GUPTA R. K. , FAUCK R. , WAKEFIELD ST J.
Published: May 2007

The value of fine catheter aspiration cytology in the diagnosis of metastatic tumours is illustrated by a case of pleomorphic giant cell carcinoma of the pancreas which had metastasized to the peritoneal cavity. the finding of unequivocal malignant cells obviated the need for further diagnostic procedures. Electron microscopy and immunostaining further substantiated the light microscopic cytodiagnosis and identified the tumour type and source of the primary tumour. Furthermore, subsequent cell block preparation from the aspirated material demonstrated the histological features of this tumour.
An Audit of Cervical Cancer Deaths In Nottingham
Authors: WILSON S. H. , JOHNSON J.
Published: May 2007

Death certificates were reviewed and 57 women were identified whose primary cause of death was cervical cancer. Their cervical smear records were reviewed from laboratory files. Only nine had participated in the cervical cancer screening programme before the diagnosis of cervical cancer was made. One woman had an abnormal smear as a result of cervical screening but failed to attend for follow‐up.

The problem of false negative smears is also addressed and the value of review of negative smears for the purposes of cytology audit is emphasized.
Measuring Proliferation In Routine Fine Needle Aspirates. Immunocytochemical Detection of Bromodeoxyuridine Incorporation and Ki‐67 Expression In Breast Aspirates
Authors: BULEY I. D. , MORRISON E. H. , KAKLAMANIS L. , HORAK E. , GATTER K. C.
Published: May 2007

Two simple quantitative means of measuring tumour proliferation which can be applied to cytological material are described. One method involves immunocytochemical staining of cytological smears prepared from breast aspirates with the monoclonal antibody Ki‐67. the other method involves incubation of aspirated material with 5‐Bromo‐2‐deoxyuridine (BrdU). Direct measurement of the S phase of the cell cycle is feasible in breast fine needle aspirates by Bromodeoxyuridine incorporation and subsequent immunocytochemical detection. the proliferation indices obtained correlate with those derived from Ki‐67 staining. This technique is suitable for routine use in the assessment of tumour proliferation.
Comparison of Four Immunochemical Methods For the Measurement of Oestrogen Receptor Levels In Breast Cancer
Authors: RYDE C. M. , SMITH D. , KING N. , TROTT P. A. , MACLENNAN K. , McKINNA J. A. , MINASIAN H. , DOWSETT M.
Published: May 2007

Four methods of assessing oestrogen receptor (ER) status were compared in 33 patients with operable primary breast cancer. the methods used to assess the ER status were immunocyto‐chemical assay (ER‐ICA) of frozen sections, fine needle aspirates and imprint material and enzyme immunoassay (ER‐EIA) of tumour tissue. A mean overall ER positivity of 45% (15 out of 33), 41 % (13 out of 32) and 21 % (six out of 29) was obtained by immunocytochemical (ER‐ICA) staining of frozen sections, fine needle aspirates and tumour imprints, respectively, and a mean overall ER positivity of 42% (14 out of 33) was obtained by ER‐EIA. the concordance of ER positivity in pairs of data obtained from different method combinations was found to range between 72 and 91%. However, statistically there was no significant difference between the four methods on the basis of the data obtained. Good comparability has been shown between the three tissue analyses and therefore the method of choice is technically not immediately apparent.
Fine Needle Aspiration Cytology of Cutaneous Vascular Tumours
Authors: PÉREZ‐GUILLERMO M. , PÉREZ J. SOLA , ROJO B. GARCÍA , GIL A. HERNÁNDEZ
Published: May 2007

We have studied 12 cutaneous vascular tumours by means of fine‐needle aspiration cytology (FNAC): six capillary haemangiomas, one cavernous haemangioma, one Masson's pseudoangiosarcoma, two angiosarcomas, one benign haemangioendothelioma and one glomus tumour. We describe the main cytopathological findings and we discuss the differential diagnosis in each case. We consider that the cytopathological findings of the above lesions, evaluated in the context of the clinical findings, are sufficiently characteristic for us to be able to make a definitive diagnosis. We believe that FNAC can play an important part in the diagnosis and therapeutic planning of these tumours.
Cytological Appearances of A Solitary Squamous Cell Papilloma With Associated Mucous Gland Adenoma In the Lung
Authors: BRIGHTMAN I. , MORGAN J. A. , ZWEHL D. V. , SHEPPARD M. N.
Published: May 2007

Solitary papillomas of the lung are rare. They are usually squamous but mixed squamous cell papilloma and mucous gland adenoma can occur. We report for the first time the Cytological findings of a fine needle aspirate from a mixed squamous cell papilloma and mucous gland adenoma from the lung periphery.
Partial Rescreening of All Negative Smears: an Improved Method of Quality Assurance In Laboratories Undertaking Cervical Screening
Authors: FARAKER C. A.
Published: May 2007

Partial rescreening was carried out on 9633 cervical smears reported as negative by standard screening. Each slide was ‘step‐screened’ at normal speed for 30 s. Thirteen false negative smears were detected by this method. No false negatives were revealed by conventionally rescreening 10% of the same study group. the sensitivity of the method was assessed by ‘step‐screening’ 100 known positive smears. of this group 92 were detected. the results indicate that partial rescreening is a sensitive method of quality assurance and should replace conventional 10% proportional rescreening, which is ineffective.
Laboratory Test of an Automated Cell Analysis System For Cervical Screening
Authors: STROHMEIER R. , NAUJOKS H. , VAN DRIEL‐KULKER A. M. J. , PLOEM J. S.
Published: May 2007

An automated cell analysis system (Autoplan‐MIAC) for the early detection of precancerous lesions of the cervix was tested under semi‐routine conditions in a clinical cytology laboratory. A set of 1500 specimens, highly enriched with abnormal cases, was analysed. Cervical scrapings were collected in suspension and processed by cytocentrifugation for microscopy. Two slides were prepared from each sample: one for staining according to Papanicolaou for the visual reference diagnosis and one for Feulgen staining for automated analysis. the specimens were evaluated in two ways: the first one, which is referred to as the automated machine classification system (AMC), classifies the specimens according to the number and ratio of selected objects (alarms) and is a fully automated system. the second system classifies the specimens after visual evaluation of the stored alarms as they are displayed on a TV monitor, and is designated the interactive machine classification system (IMC). the AMC results showed a false positive rate of 16.5% when the cut‐off threshold was selected so that all 117 positively diagnosed specimens were classified ‘positive’ by the system. In that case 87.4% of the CINI and 96.9% of the CINII cases were AMC‐positive. the IMC results showed a false positive rate of 2.5%, when 86.3% of the CIN I cases, 96.9% of the CIN II cases and all CIN III and invasive carcinoma cases were positively classified.
Evidence That the Sensitivity Is Increased and the Inadequacy Rate Decreased When Pathologists Take Aspirates For Cytodiagnosis
Authors: PADEL A. F. , COGHILL S. B. , POWIS S. J. A.
Published: May 2007

The results of the diagnostic accuracy of breast fine needle aspiration specimens taken by the pathologist in a joint surgical clinic are compared with those taken by a surgeon. In the joint clinic the complete sensitivity rose by 15% and the number of missed malignancies fell by half.
Comparison of Monoclonal Antibodies Aua1 and Ber Ep4 With Anti‐Cea For Detecting Carcinoma Cells In Serous Effusions and Distinguishing Them From Mesothelial Cells
Authors: ROBINSON R. J. , ROYSTON D.
Published: May 2007

Commercially available monoclonal antibodies AUA1, BER EP4 and carcinoembryonic antigen (CEA) were applied to cell blocks from 95 serous effusions. AUA1 and BER EP4 were reactive with 89% of effusions known to contain carcinoma cells, and anti‐CEA with 71%. They also reacted with cells in two effusions from patients with malignant disease which were regarded as negative on conventional cytological examination of Papanicolaou‐stained smears. They were negative in all but one of the benign effusions. Using all three antibodies, 95% of effusions containing carcinoma cells were detected. Use of these antibodies could improve the cytological diagnosis of serous effusions.
Borderline Nuclear Abnormality In Cervical Smears: A Cytological Review of 200 Cases With Histological Correlation
Authors: STEWART C. J. R. , LIVINGSTONE D. , MUTCH A. F.
Published: May 2007

The cervical cytology and histology specimens from 200 patients referred to colposcopy with borderline nuclear abnormality were reviewed. Human papillomavirus (HPV)‐associated changes were identified in 103 of 200 (53%) referral smears and in 139 of 150 (91%) biopsy specimens. Cervical intraepithelial neoplasia (CIN) was less frequently diagnosed on review compared with the original histopathology reports (30.7%vs 45.4%); the discrepancy was largely attributable to a lower incidence of CINI. There was agreement in the grading of borderline nuclear abnormality in 161 of 200 referral smears following review. Twenty‐three smears were upgraded to mild dyskaryosis, whereas 16 were reclassified as negative.
Follow up of women with a history of mildly abnormal cervical smears which have returned to normal without treatment
Authors: HERBERT A. , GREGORY M. , WAGSTAFF H. F.
Published: May 2007

The progress of 124 women with at least two negative cervical smears following a history of mildly abnormal smears for which no treatment had been given was compared with 106 women with negative smears and a clinical history of genital warts or herpes virus infection and 460 age‐matched controls. After 4 years, excluding those for whom there was no follow up, 5.8% of those with a history of abnormal smears, none of those with a clinical history of genital warts or herpes virus and 1.1% of controls had developed histological evidence of at least cervical intraepithelial neoplasia grade III (CINIII) when referred for investigation of subsequent abnormal smears; one woman, from the control group, had developed invasive cervical cancer. Women with two negative smears after a history of abnormal smears who subsequently developed CINIII were more likely to have had a previous smear reported as moderate or mild‐moderate dyskaryosis (2/6) compared with those whose follow up was negative (2/89). the results suggest that two negative cervical smears may not necessarily indicate that a lesion has regressed, but that a clinical history of genital warts or herpes virus infection should not be an indication for increased surveillance.
Identification of aneuploid cells in cytological specimens by combined in situ hybridization and immunocytochemistry
Authors: ROBBEN H. , VAN DEKKEN H. , PODDIGHE P. J. , VOOIJS G. P.
Published: May 2007

The purpose of our study was the application of non‐isotopic in situ hybridization with chromosome‐specific repetitive DNA probes for the determination of cytogenetically aberrant cells in routine cytological materials, such as cervical smears and breast tumour aspirates. Hyperdiploid cells in fine needle aspirates (FNA) of breast tumours could be visualized by in situ hybridization with a chromosome l‐specific repetitive DNA probe. However, for the evaluation of a specific cell type in heterogeneous cell populations, i.e. cervical smears, a procedure combining immunocytochemistry and in situ hybridization can be required. Therefore, we developed a combination protocol using β‐galactosidase/ ferri‐ferrocyanide (blue‐green) for immunocytochemistry and peroxidase/DAB (brown‐black) for detection of the DNA probe. the described protocol enabled us to distinguish squamous epithelial cells within heterogeneous cell populations. By combining the chromosome 1 DNA probe with a specific cytokeratin marker it was possible to identify the chromosomal abnormal cells within cervical smears.
An Australian trial of ThinPrep: a new cytopreparatory technique
Authors: LAVERTY C. R. A. , THURLOE J. K. , REDMAN N. L. , FARNSWORTH A.
Published: May 2007

To evaluate the sensitivity and suitability of ThinPrep, a new slide preparation technique, 2026 paired cervical cytology slides were examined. After conventional Papanicolaou smears were prepared, the sampling instruments were rinsed in a fluid fixative. ThinPrep slides were then prepared in the laboratory from the surplus cells in the fixative. Compared with the Pap smears, ThinPrep slides were easier and quicker to screen, were inconclusive less often, and had similar rates for detecting abnormalities and infection. There were more unsatisfactory ThinPrep slides and more ThinPrep slides lacked endocervical cells. Both of these shortcomings were found to be linked to the choice of sampling implements. This study, in which a variety of sampling instruments was used, fails to confirm some of the previous claims made for the new technique.
Analysis of the causes of false negative cytology reports on breast cancer fine needle aspirates
Authors: CARIAGGI M. P. , BULGARESI P. , CONFORTINI M. , BONARDI L. , MADDAU C. , MATUCCI N. , CIATTO S.
Published: May 2007

Forty‐six (2.9%) false negative reports were recorded among adequate fine needle aspirates from 1609 consecutive histologically proven carcinomas, observed from 1991 to 1993. False negatives were more frequent among younger women (<40 years=7.1; 40‐49 years=4.0; 50‐59 years=3.6; 60‐69 years=1.7; >69 years=1.5%), lobular invasive subtypes (5.4%), and smaller tumours (pT1a=4.2; pT1b=7.6; pT1c=1.9; pT2=2.1; pT3‐4=1.5%). the latter finding is probably ascribable to better differentiation and less precise sampling of small non‐palpable tumours. No significant association was found between the false negative rate and the sampler's or reader's skill and experience. the former finding may be ascribed to the wide use of sonography guided aspiration, even for palpable masses, and the latter to the fact that readers were highly experienced and undergo periodic quality control of individual performance. False negatives were reclassified at reviews as true false negatives, reading errors or inadequates in 27, 11, and eight cases, respectively. the observed findings suggest that in most cases cytological faults were due to the absence of cytological atypia in cells sampled from well differentiated tumours, rather than to misinterpretation or sampling from adjacent normal tissues.
Formation of bile canaliculi in long‐term primary cultures of adult rat hepatocytes on permeable membrane: an ultrastructural study
Authors: GUÉRY C. , SECCHI J. , VANNIER B. , FOURNEX R. , LORENZON G.
Published: May 2007

Adult rat hepatocytes were cultured for 15 days on type I collagen‐coated permeable membranes in a hormonally defined Waxman's modified medium supplemented with very low concentrations of insulin, glucagon and dexamethasone. Phase contrast examination showed that 15‐day‐old cultures still formed a regular monolayer of polygonal cells. In similarly aged cultures, intracellular glycogen was abundant and evenly distributed, while steatosis remained very limited. Scanning and transmission electron microscopy showed that well developed bile canaliculi could be observed on the lateral side of the hepatocyte membrane after 4 days of incubation and persisted for 2 weeks. These canalicular structures probably originated from coalescence of membrane invaginations observed in 1‐day‐old cultures. Transmission electron microscopy showed that the ultrastructure of the cells was very close to that of normal rat hepatocytes in the intact liver. These results suggest that rat hepatocytes cultured under these experimental conditions are able to develop and maintain tissue‐specific cytochemical and morphological properties for at least 15 days.
Quality grading for cervical smears
Authors: WADEHRA V. , SANKAR K.
Published: May 2007

Three thousand five hundred and eighty cervical smears were taken in 1990–1992 at a Genitourinary Medicine Clinic with various spatula or spatula brush combinations. the unsatisfactory rate and the detection of cellular abnormalities showed some relation to spatula type. However, the satisfactory smears screened in the laboratory are routinely assigned a quality grade‐good, fair or poor. Analysis shows higher rate of detection of cellular abnormalities in good quality smears, the detection of dyskaryosis being twice as high, in contrast to the fair or poor quality smears. It is suggested that quality grade is a better way of classifying smear quality in the cervical screening programmes rather than the presence or absence of endocervical and/or metaplastic cells.
The detection of endocervical gland involvement by high grade squamous intraepithelial lesions in smears prepared from endocervical brush specimens
Authors: VAN HOEVEN K. H. , HANAU C. A. , HUDOCK J. A.
Published: May 2007

The cytologic features of squamous cell carcinoma in situ with endocervical gland involvement have been described in cervical smears. We evaluated the presence of two types of cellular fragments in 43 cervical smears of high grade squamous intraepithelial lesions (HGSIL) to assess their ability to predict glandular involvement by HGSIL in subsequent cone biopsies. an endocervical brush was used to obtain all endocervical specimens. of 16 cases without glandular involvement, fragments were present in 13 smears. of 27 cases with glandular involvement, fragments were absent in 11 smears. No statistical association was identified between the presence of abnormal cellular fragments on cervical smears of HGSIL and endocervical gland involvement on cone biopsies.
UK national audit of breast fine needle aspiration cytology in 1990–91: diagnostic criteria
Authors: HUNT C. M. , WILSON S. , PINDER S. E. , ELSTON C. W. , ELLIS I. O.
Published: May 2007

A survey into the practice of fine needle aspiration cytology of the breast amongst members of the British Society for Clinical Cytology in 1990 and 1991 was performed. This paper presents their reported use of diagnostic categories in reporting and the criteria found useful in the diagnosis of benign and malignant disease. A wide variety of diagnostic categories are in use. the criteria used in diagnosis largely follow recommendations found in standard textbooks, but some less well recognized features were also suggested.
Shelter availability affects behaviour, size‐dependent and mean growth of juvenile Atlantic salmon
Authors: FINSTAD A. G. , EINUM S. , FORSETH T. , UGEDAL O.
Published: May 2007

1. Anthropogenic disturbances of the physical habitat and corresponding effects on fish performance are key issues in stream conservation and restoration. Reduced habitat complexity because of increased sediment loadings and canalization is of particular importance, but it is not clear to what extent fish populations are influenced directly by changes in the physical environment, or indirectly through changes in the biotic environment affecting the food availability.

2. Here, we test for the direct effect of habitat complexity on the performance (growth) of juvenile Atlantic salmon by manipulating shelter availability (interstitial spaces in the substrate) across 20 semi‐natural stream channels without altering the substrate composition, and stocking each channel with a common density of fish. A simple method for measuring salmonid shelters using flexible PVC tubes was developed and tested. Daytime sheltering behaviour and growth rates were compared across the channels differing in shelter availability.

3. Measured shelter availability was strongly negatively correlated with observed number of fish not finding shelters and mass loss rates of the fish (growth performance) increased with decreasing number of measured shelters. Number and mean depth of interstitial spaces explained up to 68% and 24% of the among‐channel variation in sheltering behaviour and growth performance, respectively. Furthermore, negative effects of shelter reduction increased with fish body size. Thus, changes in habitat structure may even influence the size selection gradients.

4. Shelter availability is an easily measured variable, possibly affecting the population demographics and long‐term evolutionary processes, and is therefore a key habitat factor to be considered in stream restoration and habitat classification.
Responses of taxonomic distinctness and species diversity indices to anthropogenic impacts and natural environmental gradients in stream macroinvertebrates
Authors: HEINO JANI , MYKRÄ HEIKKI , HÄMÄLÄINEN HEIKKI , AROVIITA JUKKA , MUOTKA TIMO
Published: May 2007

1. Many studies have shown traditional species diversity indices to perform poorly in discriminating anthropogenic influences on biodiversity. By contrast, in marine systems, taxonomic distinctness indices that take into account the taxonomic relatedness of species have been shown to discriminate anthropogenic effects. However, few studies have examined the performance of taxonomic distinctness indices in freshwater systems.

2. We studied the performance of four species diversity indices and four taxonomic distinctness indices for detecting anthropogenic effects on stream macroinvertebrate assemblages. Further, we examined the effects of catchment type and area, as well as two variables (pH and total phosphorus) potentially describing anthropogenic perturbation on biodiversity.

3. We found no indications of degraded biodiversity at the putatively disturbed sites. However, species density, rarefied species richness, Shannon's diversity and taxonomic diversity showed higher index values in streams draining mineral as opposed to peatland catchments.

4. Of the major environmental gradients analysed, biodiversity indices showed the strongest relationships with catchment area, lending further support to the importance of stream size for macroinvertebrate biodiversity. Some of the indices also showed weak linear and quadratic relationships to pH and total phosphorus, and residuals from the biodiversity index‐catchment area regressions (i.e. area effect standardized) were more weakly related to pH and total phosphorus than the original index values.

5. There are a number of reasons why the biodiversity indices did not respond to anthropogenic perturbation. First, some natural environmental gradients may mask the effects of perturbation on biodiversity. Secondly, perturbations of riverine ecosystems in our study area may not be strong enough to cause drastic changes in biodiversity. Thirdly, multiple anthropogenic stressors may either increase or decrease biodiversity, and thus the coarse division of sites into reference and altered streams may be an oversimplification.

6. Although neither species diversity nor taxonomic distinctness indices revealed anthropogenic degradation of macroinvertebrate assemblages in this study, the traditional species diversity and taxonomic distinctness indices were very weakly correlated. Therefore, we urge that biodiversity assessment and conservation planning should utilize a number of different indices, as they may provide complementary information about biotic assemblages.