bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular cloning and characterization of a nuclear androgen receptor activated by 11-ketotestosterone
Authors: Olsson Per-Erik , Berg A Håkan , von Hofsten Jonas , Grahn Birgitta , Hellqvist Anna , Larsson Anders , Karlsson Johnny , Modig Carina , Borg Bertil , Thomas Peter 
Published: August 2005

Abstract
Although 11-ketotestosterone is a potent androgen and induces male secondary sex characteristics in many teleosts, androgen receptors with high binding affinity for 11-ketotestosterone or preferential activation by 11-ketotestosterone have not been identified. So, the mechanism by which 11-ketotestosterone exhibits such high potency remains unclear. Recently we cloned the cDNA of an 11-ketotestosterone regulated protein, spiggin, from three-spined stickleback renal tissue. As spiggin is the only identified gene product regulated by 11-ketotestosterone, the stickleback kidney is ideal for determination of the mechanism of 11-ketotestosterone gene regulation. A single androgen receptor gene with two splicing variants, belonging to the androgen receptor-β subfamily was cloned from stickleback kidney. A high affinity, saturable, single class of androgen specific binding sites, with the characteristics of an androgen receptor, was identified in renal cytosolic and nuclear fractions. Measurement of ligand binding moieties in the cytosolic and nuclear fractions as well as to the recombinant receptor revealed lower affinity for 11-ketotestosterone than for dihydrotestosterone. Treatment with different androgens did not up-regulate androgen receptor mRNA level or increase receptor abundance, suggesting that auto-regulation is not involved in differential ligand activation. However, comparison of the trans-activation potential of the stickleback androgen receptor with the human androgen receptor, in both human HepG2 cells and zebrafish ZFL cells, revealed preferential activation by 11-ketotestosterone of the stickleback receptor, but not of the human receptor. These findings demonstrate the presence of a receptor preferentially activated by 11-ketotestosterone in the three-spined stickleback, so far the only one known in any animal.
Collection of population-based cancer staging information in Western Australia – a feasibility study
Authors: Threlfall Timothy , Wittorff Jana , Boutdara Padabphet , Heyworth Jane , Katris Paul , Sheiner Harry , Fritschi Lin 
Published: August 2005

Abstract

Background
Routine data from cancer registries often lack information on stage of cancer, limiting their use. This study aimed to determine whether or not it is feasible to add cancer staging data to the routine data collections of a population-based Western Australian Cancer Registry (WACR).

Methods
For each of the five most common cancer types (prostate, colorectal, melanoma, breast and lung cancers), 60 cases were selected for staging. For the 15 next most common cancer types, 20 cases were selected. Four sources for collecting staging data were used in the following order: the WACR, the hospital based cancer registries (HBCRs), hospital medical records, and letters to treating doctors. If the case was unable to be fully staged, due to lack of information on regional lymph node invasion or distant metastases, we made the following assumptions. Cases which had data available for tumour (T) and regional lymph nodes (N), but no assessment of distant metastasis (MX) were assumed to have no distant metastases (M0). Cases which had data for T and M, but no assessment of regional nodal involvement (NX) were assumed to have no regional nodal involvement (N0).

Results
The main focus of this project was the process of collecting staging data, and not the outcomes. For ovary, cervix and uterus cancers the existence of a HBCR increased the stageable proportion of cases so that staging data for these cancers could be incorporated into the WACR immediately. Breast and colorectal cancer could also be staged with adequate completeness if it were assumed that MX = M0. Similarly, melanoma and prostate cancer could be staged adequately if it were assumed that NX = N0 and MX = M0. Some cases of stomach, lung, pancreas, thyroid, testis and kidney cancers could be staged, but additional clinical input – on pathology request forms, for example – would be required to achieve useable levels of completeness. For the remaining cancer types either staging is widely regarded as not relevant, and no generally-accepted system exists, or an acceptable level of completeness is not achievable.

Conclusion
Adding stage to routinely collected information in a cancer registry is possible for many cancer types, particularly if the assumptions regarding missing data are found to be acceptable or if the guidelines for MX = M0 asumptions are clarified. These findings should be generalizable to most cancer registries in developed countries, if hospital-based cancer registries or other specialized databases are accessible.
Successful myomectomy during pregnancy : A case report
Authors: Umezurike Chisara , Feyi-Waboso Paul 
Published: August 2005

Abstract
Background
The medical literature has reported an increase in myomectomy during caesarean section in the past decade. However, myomectomy performed during pregnancy remains a rarity. The management of uterine fibroids during pregnancy is usually expectant and surgical removal is generally delayed until after delivery. We present a case of a large, symptomatic uterine fibroid diagnosed during pregnancy which was successfully managed by antepartum myomectomy.

Case presentation
A 30 year old woman presented with a one year history of abdominal swelling, amenorrhea and severe epigastric discomfort of 19 weeks duration. The abdomen was grossly distended and tense. A sonographic diagnosis of ovarian tumor in pregnancy was made. Laparotomy revealed a 32 cm degenerating subserosal uterine fibroid co-existing with an intrauterine pregnancy. Myomectomy was successfully performed. The subsequent antenatal period was uneventful with a spontaneous vaginal delivery of a female baby at 38 weeks.

Conclusion
This report supports other studies and case series that have demonstrated the safety of myomectomy during pregnancy in selected circumstances.
Mimivirus relatives in the Sargasso sea
Authors: Ghedin Elodie , Claverie Jean-Michel 
Published: August 2005

Abstract
The discovery and genome analysis of Acanthamoeba polyphaga Mimivirus, the largest known DNA virus, challenged much of the accepted dogma regarding viruses. Its particle size (>400 nm), genome length (1.2 million bp) and huge gene repertoire (911 protein coding genes) all contribute to blur the established boundaries between viruses and the smallest parasitic cellular organisms. Phylogenetic analyses also suggested that the Mimivirus lineage could have emerged prior to the individualization of cellular organisms from the three established domains, triggering a debate that can only be resolved by generating and analyzing more data. The next step is then to seek some evidence that Mimivirus is not the only representative of its kind and determine where to look for new Mimiviridae. An exhaustive similarity search of all Mimivirus predicted proteins against all publicly available sequences identified many of their closest homologues among the Sargasso Sea environmental sequences. Subsequent phylogenetic analyses suggested that unknown large viruses evolutionarily closer to Mimivirus than to any presently characterized species exist in abundance in the Sargasso Sea. Their isolation and genome sequencing could prove invaluable in understanding the origin and diversity of large DNA viruses, and shed some light on the role they eventually played in the emergence of eukaryotes.
Development of an in vitro cleavage assay system to examine vaccinia virus I7L cysteine proteinase activity
Authors: Byrd Chelsea M , Hruby Dennis E 
Published: August 2005

Abstract
Through the use of transient expression assays and directed genetics, the vaccinia virus (VV) I7L gene product has been implicated as the major maturational proteinase required for viral core protein cleavage to occur during virion assembly. To confirm this hypothesis and to enable a biochemical examination of the I7L cysteine proteinase, an in vitro cleavage assay was developed. Using extracts of VV infected cells as the source of enzyme, reaction conditions were developed which allowed accurate and efficient cleavage of exogenously added core protein precursors (P4a, P4b and P25K). The cleavage reaction proceeded in a time-dependent manner and was optimal when incubated at 25°C. I7L-mediated cleavage was not affected by selected inhibitors of metalloproteinases, aspartic acid proteinases or serine proteinases (EDTA, pepstatin, and PMSF, respectively), but was sensitive to several general cysteine proteinase inhibitors (E-64, EST, Iodoacetic acid, and NEM) as well as the I7L active site inhibitor TTP-6171 [C. Byrd et al., J. Virol. 78:12147–12156 (2004)]. Finally, in antibody pull down experiments, it could be demonstrated that monospecific αI7L serum depleted the enzyme activity whereas control sera including αG1L, directed against the VV metalloproteinase, did not. Taken together, these data provide biochemical evidence that I7L is a cysteine proteinase which is directly involved in VV core protein cleavage. Furthermore, establishment of this I7L-mediated in vitro cleavage assay should enable future studies into the enzymology and co-factor requirements of the proteolysis reaction, and facilitate antiviral drug development against this essential target.
International Committee on Taxonomy of Viruses and the 3,142 unassigned species
Authors: Fauquet CM , Fargette D 
Published: August 2005

Abstract
In 2005, ICTV (International Committee on Taxonomy of Viruses), the official body of the Virology Division of the International Union of Microbiological Societies responsible for naming and classifying viruses, will publish its latest report, the state of the art in virus nomenclature and taxonomy. The book lists more than 6,000 viruses classified in 1,950 species and in more than 391 different higher taxa. However, GenBank contains a staggering additional 3,142 "species" unaccounted for by the ICTV report. This paper reviews the reasons for such a situation and suggests what might be done in the near future to remedy this problem, particularly in light of the potential for a ten-fold increase in virus sequencing in the coming years that would generate many unclassified viruses. A number of changes could be made both at ICTV and GenBank to better handle virus taxonomy and classification in the future.
Cytokine release from alveolar macrophages exposed to ambient particulate matter: Heterogeneity in relation to size, city and season
Authors: Hetland Ragna B , Cassee Flemming R , Låg Marit , Refsnes Magne , Dybing Erik , Schwarze Per E 
Published: August 2005

Abstract

Background
Several studies have demonstrated an association between exposure to ambient particulate matter (PM) and respiratory and cardiovascular diseases. Inflammation seems to play an important role in the observed health effects. However, the predominant particle component(s) that drives the inflammation is still not fully clarified. In this study representative coarse (2.5–10 μm) and fine (0.1–2.5 μm) particulate samples from a western, an eastern, a northern and a southern European city (Amsterdam, Lodz, Oslo and Rome) were collected during three seasons (spring, summer and winter). All fractions were investigated with respect to cytokine-inducing potential in primary macrophages isolated from rat lung. The results were related to the physical and chemical parameters of the samples in order to disclose possible connections between inflammatory potential and specific characteristics of the particles.

Results
Compared on a gram-by gram basis, both site-specific and seasonal variations in the PM-induced cytokine responses were demonstrated. The samples collected in the eastern (Lodz) and southern (Rome) cities appeared to be the most potent. Seasonal variation was most obvious with the samples from Lodz, with the highest responses induced by the spring and summer samples. The site-specific or seasonal variation in cytokine release could not be attributed to variations in any of the chemical parameters. Coarse fractions from all cities were more potent to induce the inflammatory cytokines interleukin-6 and tumour necrosis factor-α than the corresponding fine fractions. Higher levels of specific elements such as iron and copper, some polycyclic aromatic hydrocarbons (PAHs) and endotoxin/lipopolysaccaride seemed to be prevalent in the coarse fractions. However, variations in the content of these components did not reflect the variation in cytokine release induced by the different coarse fractions. Addition of polymyxin B did not affect the particle-induced cytokine release, indicating that the variations in potency among the coarse fractions are not explained by endootoxin.

Conclusion
The inflammatory potential of ambient PM demonstrated heterogeneity in relation to city and season. The coarse particle fractions were consistently more potent than the respective fine fractions. Though a higher level of some elements, PAH and endotoxin was found in the coarse fractions, the presence of specific components was not sufficient to explain all variations in PM-induced cytokine release.
Adaption to life at high salt concentrations in Archaea, Bacteria and Eukarya
Authors: Rensing Christopher 
Published: August 2005

Abstract
The diversity of hypersaline environments and the physiology of representative organisms are only beginning to be understood. Recent progress in this area is documented in "Adaptation to life at high salt concentrations in Archaea, Bacteria, and Eukarya" – eds. Nina Gunde-Cimerman, Aharon Oren and Ana Plemenitas. The 34 chapters successfully paint a fascinating emerging picture of these environments and the microorganisms inhabiting them.
Plant Methods: putting the spotlight on technological innovation in the plant sciences
Authors: Forde Brian G , Roberts Michael R 
Published: August 2005

Abstract

Plant Methods is a new journal for plant biologists, specialising in the rapid publication of peer-reviewed articles with a focus on technological innovation in the plant sciences. The aim of Plant Methods is to stimulate the development and adoption of new and improved techniques and research tools in plant biology. We hope to promote more consistent standards in the plant sciences, and make readily accessible laboratory and computer-based research tools available to the whole community. This will be achieved by publishing Research articles, Methodology papers and Reviews using the BioMed Central Open Access publishing model. The journal is supported by a prestigious editorial board, whose members all recognise the importance of technological innovation as a driver for basic science.
High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis
Authors: Cryer Nicholas C , Butler David R , Wilkinson Mike J 
Published: August 2005

Abstract

Background
Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers.

Results
Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool.

Conclusion
The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays.
Application of a population-based severity scoring system to individual patients results in frequent misclassification
Authors: Booth Frank V , Short Mary , Shorr Andrew F , Arkins Nancy , Bates Becky , Qualy Rebecca L , Levy Howard 
Published: August 2005

Abstract
Introduction
APACHE II (AP2) was developed to allow a systematic examination of intensive care unit outcomes in a risk adjusted manner. AP2 has been widely adopted in clinical trials to assure broad consistency amongst different groups. Although errors in calculating the true AP2 score may not be reducible below 15%, the self-canceling effect of random errors reduces the importance of such errors when applied to large populations. It has been suggested that a threshold AP2 score be used in clinical decision making for individual patients. This study reports the AP2 scoring errors of researchers involved in a large sepsis trial and models the consequences of such an error rate for individual severe sepsis patients.

Methods
Fifty-six researchers with explicit training in data abstraction and completion of the AP2 score received scenarios consisting of composites of real patient histories. Descriptive statistics were calculated for each scenario. The standard deviations were calculated compared with an adjudicated score. Intraclass correlations for inter-observer reliability were performed using Shrout-Fleiss methodology. Theoretical distribution curves were calculated for a broad range of AP2 scores using standard deviations of 6, 9 and 12. For each curve, the misclassification rate was determined using an AP2 score cut-off of ≥25. The percentage of misclassifications for each true AP2 score was then applied to the corresponding AP2 score obtained from the PROGRESS severe sepsis registry.

Results
The error rate for the total AP2 score was 86% (individual variables were in the range 10% to 87%). Intraclass correlation for the inter-observer reliability was 0.51. Of the patients from the PROGRESS registry. 50% had AP2 scores in the range 17 to 28. Within this interquartile range, 70% to 85% of all misclassified patients would reside.

Conclusion
It is more likely that an individual patient will be scored incorrectly than correctly. The data obtained from the scenarios indicated that as the true AP2 score approached an arbitrary cut-off point of 25, the observed misclassification rate increased. Integrating our study of AP2 score errors with the published literature leads us to conclude that the AP2 is an inappropriate sole tool for resource allocation decisions for individual patients.
PubNet: a flexible system for visualizing literature derived networks
Authors: Douglas Shawn M , Montelione Gaetano T , Gerstein Mark 
Published: August 2005

AbstractWe have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors. This feature allows one to, for example, examine a literature derived network of genes based on functional similarity.
Phase II Multi-Institutional Randomized Trial of Docetaxel Plus Cisplatin With or Without Fluorouracil in Patients With Untreated, Advanced Gastric, or Gastroesophageal Adenocarcinoma
Authors: Ajani Jaffer A. , Fodor Miguel B. , Tjulandin Sergei A. , Moiseyenko Vladimir M. , Chao Yee , Filho Sebastiao Cabral , Majlis Alejandro , Assadourian Sylvie , Van Cutsem Eric 
Published: August 2005

Purpose The purpose of this study was to define the contribution of docetaxel to combination chemotherapy in the outcome of patients with advanced gastric or gastroesophageal adenocarcinoma. We compared the overall response rate (ORR) and safety of docetaxel plus cisplatin (DC) with DC plus fluorouracil (DCF) to select either DC or DCF as the experimental treatment in the ensuing phase III part of trial V-325. Patients and Methods In this phase II randomized study, untreated patients with confirmed advanced gastric or gastroesophageal adenocarcinoma received either DCF (docetaxel 75 mg/m2, cisplatin 75 mg/m2 on day 1, and fluorouracil 750 mg/m2/d as continuous infusion on days 1 to 5) or DC (docetaxel 85 mg/m2 and cisplatin 75 mg/m2 on day 1) every 3 weeks. An independent data monitoring committee (IDMC) was to select one of the two regimens based primarily on ORR and safety profile. Results Of 158 randomly assigned patients, 155 (DCF, n = 79; DC, n = 76) received treatment. The confirmed ORR was 43% for DCF (n = 79) and 26% for DC (n = 76). Median time to progression was 5.9 months for DCF and 5.0 months for DC. Median overall survival time was 9.6 months for DCF and 10.5 months for DC. The most frequent grade 3 and 4 events per patient included neutropenia (DCF = 86%; DC = 87%) and GI (DCF = 56%; DC = 30%). Conclusion Both regimens were active, but DCF produced a higher confirmed ORR than DC. Toxicity profiles of DCF were considered manageable. The IDMC chose DCF for the phase III part of V-325, which compares DCF with cisplatin plus fluorouracil.
αvβ3-integrin-dependent activation of focal adhesion kinase mediates NF-κB activation and motogenic activity by HIV-1 Tat in endothelial cells
Authors: Urbinati Chiara , Bugatti Antonella , Giacca Mauro , Schlaepfer David , Presta Marco , Rusnati Marco 
Published: August 2005

Once in the extracellular environment, the transactivator protein HIV-1 Tat exerts several pleiotropic effects by interacting with different cellular receptors, including integrin αvβ3. Real-time surface plasmon resonance analysis reveals that Tat/αVβ3 interaction occurs with rapid kinetics (association and dissociation rates equal to 1.16×107 M-1 s-1 and 3.78×10-1 s-1, respectively) and high affinity (dissociation constant = 32 nM). Through this interaction, substratum-immobilized Tat promotes adhesion and motogenic activity in endothelial cells. Also, αvβ3/Tat interaction triggers the activation of focal adhesion kinase, RhoA and pp60src. Overexpression of the dominant negative form of focal adhesion kinase, but not of an inactive Leu1034Ser substitution mutant isoform, impairs the activation of focal adhesion kinase and RhoA, but not that of pp60src, without affecting endothelial cell adhesion and spreading. αvβ3/Tat interaction triggers the activation of NF-κB in endothelial cells in a focal adhesion kinase-, RhoA- and pp60src-dependent manner, as shown in dominant negative focal adhesion kinase transfectants or using specific pharmacological inhibitors. Finally, the activation of focal adhesion kinase, RhoA, NF-κB and pp60src are required to mediate the motogenic activity of Tat in endothelial cells.Since Tat accumulates in an immobilized form in the extracellular matrix, these results provide new biochemical and biological insights about αvβ3/Tat interaction exploitable for the design of anti-Tat strategies.