bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of aggregate mortality risk on defined benefit pension plans
Authors: DUSHI IRENA , FRIEDBERG LEORA , WEBB TONY 
Published: March 2010

AbstractWe calculate the risk faced by defined benefit plan providers arising from uncertain aggregate mortality – the risk that the average participant will live longer than expected. First, comparing the widely cited Lee–Carter model to industry benchmarks that are commonly employed by plan providers, we show that these benchmarks appear to substantially underestimate longevity. The resultant understatement of liabilities may reach 12.2% for typical male participants in defined benefit plans and may reach 22.4% for male workers aged 22. Next, we consider consequences for plan liabilities if aggregate mortality declines unexpectedly faster than is predicted by a putatively unbiased projection. There is a 5% chance that liabilities of a terminated plan would be 3.1% to 5.3% higher than what is expected, depending on the mix of workers covered.
Case-Crossover Study of Burkholderia cepacia Complex Bloodstream Infection
Associated with Contaminated Intravenous Bromopride
Authors: Martins Ianick Souto , Pellegrino Flávia Lúcia Piffano Costa , Freitas Andrea d'Avila , da Silva Santos Marisa , Ferraiuoli Giovanna lanini d'Alemeida , Vasques Màrcia Regina Guimarães , Amorim Efigenia Lourdes Teixeira , Oliveira Sandra , Nouér Simone Aranha , Cardoso Fernando Luiz Lopes , Mascarenhas Luiz Affonso , Magalhães Ana Cristina Gouveia , Cleinman Isabella Barbosa , Figueiredo Agnes Marie Sá , Moreira Beatriz Meurer 
Published: March 2010

Objective.
To investigate an outbreak of healthcare-associated
Burkholderia cepacia complex (BCC) primary
bloodstream infections (BCC-BSI).

Design and Setting.
Case-crossover study in a public hospital, a university hospital and a
private hospital in Rio de Janeiro, Brazil, from March 2006 to May
2006.

Patients.
Twenty-five patients with BCC-BSI.

Design.
After determining the date BCC-BSI symptoms started for each patient, 3
time intervals of data collection were defined, each one with a duration of 3
days: the case period, starting just before BCC-BSI symptoms onset; the control
period, starting 6 days before BCC-BSI symptoms onset; and the washout period,
comprising the 3 days between the case period and the control period. Exposures
evaluated were intravascular solutions and invasive devices and procedures.
Potential risk factors were identified by using the McNemar
χ2 adjusted test. Cultures of samples of potentially
contaminated solutions were performed. BCC strain typing was performed by
pulsed-field gel electrophoresis using
Spel.

Results.
The statistical analysis revealed that the use of bromopride and dipyrone
was associated with BCC-BSI. A total of 21 clinical isolates from 17 (68%) of
the 25 patients and an isolate obtained from the bromopride vial were available
for strain typing. Six pulsotypes were detected. A predominant pulsotype (A)
accounted for 11 isolates obtained from 11 patients (65%) in the 3 study
hospitals.

Conclusion.
Our investigation, using a case-crossover design, of an outbreak of
BCC-BSI infections concluded it was polyclonal but likely caused by infusion of
contaminated bromopride. The epidemiological finding was validated by
microbiological analysis. After recall of contaminated bromopride vials by the
manufacturer, the outbreak was controlled.
Statistical expression deconvolution from mixed tissue samples
Authors: Clarke Jennifer , Seo Pearl , Clarke Bertrand 
Published: March 2010

Abstract
Motivation: Global expression patterns within cells are used for purposes ranging from the identification of disease biomarkers to basic understanding of cellular processes. Unfortunately, tissue samples used in cancer studies are usually composed of multiple cell types and the non-cancerous portions can significantly affect expression profiles. This severely limits the conclusions that can be made about the specificity of gene expression in the cell-type of interest. However, statistical analysis can be used to identify differentially expressed genes that are related to the biological question being studied.
Results: We propose a statistical approach to expression deconvolution from mixed tissue samples in which the proportion of each component cell type is unknown. Our method estimates the proportion of each component in a mixed tissue sample; this estimate can be used to provide estimates of gene expression from each component. We demonstrate our technique on xenograft samples from breast cancer research and publicly available experimental datasets found in the National Center for Biotechnology Information Gene Expression Omnibus repository.
Availability: R code (http://www.r-project.org/) for estimating sample proportions is freely available to non-commercial users and available at http://www.med.miami.edu/medicine/x2691.xml
Contact: jclarke@med.miami.edu
An extended IUPAC nomenclature code for polymorphic nucleic acids
Authors: Johnson Andrew D. 
Published: March 2010

Abstract
The International Union of Pure and Applied Chemistry (IUPAC) code specified nearly 25 years ago provides a nomenclature for incompletely specified nucleic acids. However, no system currently exists that allows for the informatics representation of the relative abundance at polymorphic nucleic acids (e.g. single nucleotide polymorphisms) in a single specified character, or a string of characters. Here, I propose such an information code as a natural extension to the IUPAC nomenclature code, and present some potential uses and limitations to such a code. The primary anticipated use of this extended nomenclature code is to assist in the representation of the rapidly growing space of information in human genetic variation.
Contact: johnsonad2@nhlbi.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Can recreational scuba divers alter natural gross sedimentation rate? A case study from a Mediterranean deep cave
Authors: Di Franco Antonio , Ferruzza Gaetano , Baiata Pasquale , Chemello Renato , Milazzo Marco 
Published: March 2010

Abstract
Di Franco, A., Ferruzza, G., Baiata, P., Chemello, R., and Milazzo, M. 2010. Can recreational scuba divers alter natural gross sedimentation rate? A case study from a Mediterranean deep cave. – ICES Journal of Marine Science, 67: 871–874. Submarine caves are environments with features distinguishing them from other littoral habitats but, despite their ecological importance, their response to anthropogenic disturbance has been seldom verified. One potential threat affecting natural communities within caves is represented by recreational scuba diving. Divers' disturbance within marine caves is mainly related to physical contacts and increased sediment resuspension potentially affecting sessile organisms. The aim was to assess the potential effect of recreational divers' frequentation on the natural gross sedimentation rate (GSR) in a Mediterranean deep-water cave. To achieve this, sediment traps were deployed along a scuba trail before, during, and after the peak season for tourist-related diving. No effects of divers' frequentation were evident in terms of alteration of natural GSR, but findings will need to be validated for other caves to asses whether potential disturbance depends on frequentation levels and/or cave characteristics, i.e. sediment grain size or cave depth.
Genetic variation and spatial autocorrelation among young-of-the-year red snapper (Lutjanus campechanus) in the northern Gulf of Mexico
Authors: Saillant Eric , Bradfield S. Coleen , Gold John R. 
Published: March 2010

AbstractSaillant, E., Bradfield, S. C., and Gold, J. R. 2010. Genetic variation and spatial autocorrelation among young-of-the-year red snapper (Lutjanus campechanus) in the northern Gulf of Mexico. – ICES Journal of Marine Science, 67: 1240–1250. Temporal and spatial genetic variations at 18 nuclear-encoded microsatellites were assayed among age-0 Gulf red snapper (Lutjanus campechanus), sampled from the 2004 and 2005 cohorts in each of five regions in the northern Gulf of Mexico (Gulf) and from a mixed-age group sampled off northwest Florida. Hierarchical analysis of molecular variance revealed genetic heterogeneity among habitat patches within regions, but not among regions. A significant, positive spatial autocorrelation of microsatellite genotypes among fish sampled within the geographic range 50–100 km was detected. Bayesian coalescent analysis of historical demography indicated a decline of nearly an order of magnitude in the effective population size for red snapper across the area surveyed. The highest posterior probability for the current effective population size was 2163, approximately four orders of magnitude smaller than the estimates of red snapper census size. The results of the study demonstrate that spatial genetic structuring among young-of-the-year red snapper in the Gulf occurs at small geographic scales and is consistent with a metapopulation stock-structure model of partially connected populations. This accentuates the importance of maintaining healthy local spawning populations of red snapper in all regions across the northern Gulf.
The cytomorphologic spectrum of Wilms tumour on fine needle aspiration: a single institutional experience of 110 cases
Authors: Nayak A. , Iyer V. K. , Agarwala S. 
Published: March 2010

A. Nayak, V.K. Iyer and S. Agarwala  The cytomorphologic spectrum of Wilms tumour on fine needle aspiration: a single institutional experience of 110 casesObjective:  To analyse the cytomorphologic spectrum of Wilms tumour (WT) on aspirates, the largest series reported to date.Study design:  Adequate aspirates from paediatric renal tumours over a period of 17 years were reviewed and selected if subsequent excision showed WT or aspirates were diagnostic for WT and clinical/radiological evidence consistent with that diagnosis. Smears were re‐examined for the proportion of components, degree of pleomorphism and mitosis.Results:  Of 110 aspirates, smears were triphasic in 44 (40.0%), biphasic (blastema and tubules) in 36 (32.7%) and monophasic (blastema alone) in 30 (27.3%). Stromal predominance was seen in 11 aspirates (10.0%) and five showed rhabdomyoblastic differentiation; all 11 were triphasic. Mean mitotic rate was 9.3/5000 cells (range 4–39/5000). Nuclear atypia not amounting to anaplasia and without atypical mitoses was seen in 15 (13.6%); these presented diagnostic problems. Two aspirates (1.8%) were considered anaplastic (unfavourable), both having atypical mitoses. Criteria similar to histology (i.e. 3‐fold or more variation in nuclear size, marked hyperchromasia with bizarre nuclei and atypical mitoses in a biphasic or triphasic aspirate) helped in distinguishing anaplastic WT. Histopathological correlation in 67 cases showed good correlation of blastemal predominance, stromal predominance and anaplastic histology with the corresponding cytology. However, 9/27 (33.3%) triphasic tumours had only blastemal cells on corresponding aspiration because of sampling error. Cytokeratin was positive in 4 of 20 aspirates with blastema alone.Conclusions:  Aspirates from WT were triphasic or biphasic in the majority (72.7%), permitting cytological diagnosis, which was improved by cytokeratin immunocytochemistry. Blastemal and stromal predominance on histology correlated well with cytology, but many triphasic tumours showed only blastema on aspiration. Anaplastic WT can be detected on aspirates using criteria similar to histology.
Neuroendocrine ductal carcinoma in situ of the breast: cytological features in 32 cases
Authors: Kawasaki T. , Nakamura S. , Sakamoto G. , Kondo T. , Tsunoda‐Shimizu H. , Ishii Y. , Nakazawa T. , Mochizuki K. , Yamane T. , Inoue M. , Inoue S. , Katoh R. 
Published: March 2010

T. Kawasaki, S. Nakamura, G. Sakamoto, T. Kondo, H. Tsunoda‐Shimizu, Y. Ishii, T. Nakazawa, K. Mochizuki, T. Yamane, M. Inoue, S. Inoue and R. Katoh  Neuroendocrine ductal carcinoma in situ of the breast: cytological features in 32 casesObjective:  The purpose of this study was to clarify the cytological features of neuroendocrine ductal carcinoma in situ (NE‐DCIS) of the breast.Methods:  We analysed the cytopathological findings in 22 fine needle aspiration (FNA) smears and 17 nipple discharge smears obtained from 32 Japanese patients with NE‐DCIS.Results:  The background of the FNA smears was clear (59%), mucoid (23%), haemorrhagic (14%) or necrotic (5%). Most of the FNA smears (95%) showed high cellularity. Characteristically, NE‐DCIS cells were loosely arranged in three‐dimensional solid clusters or singly dispersed. Well‐developed vascular cores with or without malignant cells were occasionally recognized. The tumour cells were polygonal or spindle‐shaped with a fine granular, abundant cytoplasm. Nuclei with finely granular chromatin were round or oval and often eccentrically located (plasmacytoid appearance). Mitotic figures were infrequent. Nuclear grade was estimated to be low in 86%. Most nipple discharge smears had fairly low cellularity with poorly preserved cell clusters in a markedly haemorrhagic background, although two (12%) were extremely cellular with cytological characteristics similar to those of the FNA smears. Pre‐operative cytological malignant diagnoses were made in 42% of FNA smears and 0% of nipple discharge smears. Immunohistochemistry for neuroendocrine markers (chromogranin A and synaptophysin) confirmed the neuroendocrine nature of this tumour in adequate cytological specimens.Conclusions:  NE‐DCIS has distinctive cytological features and can therefore be diagnosed as a neuroendocrine tumour in most FNAs and some nipple discharge smears by cytological examination employing immunohistochemical techniques. We emphasize that a breast lesion with these features may be in situ and not invasive, and also that there is a risk of under‐diagnosis.
Thyroid fine needle aspiration cytology: a review of the National Cancer Institute state of the science symposium
Authors: Layfield L. J. , Cibas E. S. , Baloch Z. 
Published: March 2010

L. J. Layfield, E. S. Cibas and Z. Baloch Thyroid fine needle aspiration cytology: a review of the national cancer institute state of the science symposiumIn October 2007, the National Cancer Institute (NCI) of the United States sponsored a conference reviewing the state of the science of thyroid fine needle aspiration (FNA). Multiple issues were reviewed including pre‐FNA requirements, training specifications, criteria for the selection of patients to undergo FNA, diagnostic categories and criteria, ancillary testing and post‐FNA follow‐up and treatment options. A summation of conclusions covering three of these topics, followed by a question and answer session, was subsequently presented at the 35th European Congress of Cytology (ECC) in Lisbon, Portugal in September of 2009. At the ECC, the findings of the NCI committee proposals regarding the indications for FNA of thyroid nodules, diagnostic categories and criteria, and post‐FNA options for follow‐up and treatment were discussed. Herein we review the presentations given at that conference.
Diagnostic terminology for reporting thyroid fine needle aspiration cytology: European Federation of Cytology Societies thyroid working party symposium, Lisbon 2009
Authors: Kocjan G. , Cochand‐Priollet B. , De Agustin P. P. , Bourgain C. , Chandra A. , Daneshbod Y. , Deery A. , Duskova J. , Ersoz C. , Fadda G. , Fassina A. , Firat P. , Jimenez‐Ayala B. , Karakitsos P. , Koperek O. , Matesa N. , Poller D. , Thienpont L. , Ryska A. , Schenck U. , Sauer T. , Schmitt F. , Tani E. , Toivonen T. , Tötsch M. , Troncone G. , Vass L. , Vielh P. 
Published: March 2010

G. Kocjan, B. Cochand‐Priollet, P. P. de Agustin, C. Bourgain, A. Chandra, Y. Daneshbod, A. Deery, J. Duskova, C. Ersoz, G. Fadda, A. Fassina, P. Firat, B. Jimenez‐Ayala, P. Karakitsos, O. Koperek, N. Matesa, D. Poller, L. Thienpont, A. Ryska, U. Schenck, T. Sauer, F. Schmitt, E. Tani, T. Toivonen, M. Tötsch, G. Troncone, L. Vass and P. Vielh Diagnostic terminology for reporting thyroid fine needle aspiration cytology: European Federation of Cytology Societies thyroid working party symposium, Lisbon 2009A European Federation of Cytology Societies (EFCS) working party of 28 members from 14 European countries met at the European Congress of Cytology in Lisbon in September 2009, with two observers from the USA, to discuss the need for standardising thyroid FNA nomenclature in the light of the National Institute of Cancer (NCI) recommendations resulting from the State of the Science conference in Bethesda in 2007. The data were obtained through two questionnaires sent by email and a transcript of the live discussion at the congress, which is presented in full.The surveys and discussion showed that there were currently no national terminologies for reporting thyroid FNA in the different European countries except in Italy and the UK. Personal, ‘local’, surgical pathology and descriptive terminologies were in use. All but one of the working party members agreed that thyroid FNA reporting should be standardised. Whilst almost a third would adopt the NCI Bethesda terminology, which offers the advantages of a ‘risk of cancer’ correlation and is linked to clinical recommendations, more than half favoured a translation of local terminology as the first step towards a unified nomenclature, as has been done recently in the UK. There was some disagreement about the use of: a) the six‐tiered as opposed to four or five‐tiered systems, b) the use of an indeterminate category and c) the ‘follicular neoplasm‘ category, which was felt by some participants not to be different from the ‘suspicious of malignancy‘ category.The conclusions will be passed to the different national societies of cytology for discussion, who will be asked to map their local terminologies to the Bethesda classification, observe its acceptance by clinicians and audit its correlation with outcome.
Competitive interactions between two meadow grasses under nitrogen and phosphorus limitation
Authors: Venterink Harry Olde , Güsewell Sabine 
Published: March 2010

Summary 1. Different grass species dominate grasslands fertilized with nitrogen (N) or phosphorus (P), possibly due to the impact of N : P stoichiometry on competitive interactions. How species compete for nutrients, and whether the mechanisms are similar for N and P, is still not fully understood. 2. We investigated whether the outcome of competition between Alopecurus pratensis and Agrostis capillaris depends on N : P stoichiometry, and on the ability to acquire supplied N or P. Monocultures and mixtures of the two species were grown in pots at nine combinations of N and P supply (N : P ratios 1·7, 15 and 135, all at three supply levels). After 3 months, we determined plant biomass, morphological traits and nutrient concentrations of plant tissues. 3. N : P supply ratios had similar effects on the growth of the two species but contrasting effects on their competitive strength, as assessed by comparing growth in competition to growth in monoculture: Alopecurus was the stronger competitor under N limitation (N : P ratio 1·7), whereas Agrostis was an equal or stronger competitor under P limitation (N : P ratio 135). This result resembled patterns of species distribution observed in the field. 4. The strong competitive response of Alopecurus at the low N : P supply ratio was associated with a high investment in root biomass and root length, and a high nitrogen productivity. The competitive response of Agrostis at the high N : P supply ratio was associated with low root mortality and high root phosphatase activity. 5. Our results obtained under N limitation support the pre‐emption theory in which plants with the highest root length are able to acquire more N from the soil than their competitors, and therefore can suppress their growth. Under P limitation, however, plant investment in root length could not explain competitor suppression. Here, other factors important in competition for P, such as mycorrhizal hyphal length, root longevity, or exudation rates of P releasing compounds, merit investigation.
Long foraging distances impose high costs on offspring production in solitary bees
Authors: Zurbuchen Antonia , Cheesman Stephanie , Klaiber Jeannine , Müller Andreas , Hein Silke , Dorn Silvia 
Published: March 2010

Summary 1. Solitary bees are central place foragers returning to their nests several times a day with pollen and nectar to provision their brood cells. They are especially susceptible to landscape changes that lead to an increased spatial separation of suitable nesting sites and flower rich host plant stands. While knowledge of bee foraging ranges is currently growing, quantitative data on the costs of foraging flights are very scarce, although such data are crucial to understand bee population dynamics. 2. In this study, the impact of increased foraging distance on the duration of foraging bouts and on the number of brood cells provisioned per time unit was experimentally quantified in the two pollen specialist solitary bee species Hoplitis adunca and Chelostoma rapunculi. Females nesting at different sites foraged under the same environmental conditions on a single large and movable flowering host plant patch in an otherwise host plant free landscape. 3. The number of brood cells provisioned per time unit by H. adunca was found to decrease by 23%, 31% and 26% with an increase in the foraging distance by 150, 200 and 300 m, respectively. The number of brood cells provisioned by C. rapunculi decreased by 46% and 36% with an increase in the foraging distance by 500 and 600 m, respectively. 4. Contrary to expectation, a widely scattered arrangement of host plants did not result in longer mean duration of a foraging bout in H. adunca compared to a highly aggregated arrangement, which might be due to a reduced flight directionality combined with a high rate of revisitation of already depleted flowers in the aggregated plant arrangement or by a stronger competition and disturbance by other flower visitors. 5. The results of this study clearly indicate that a close neighbourhood of suitable nesting and foraging habitats is crucial for population persistence and thus conservation of endangered solitary bee species.