bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of Somatic Deletion Analysis of Prostate Cancers and Germline Linkage Analysis of Prostate Cancer Families Reveals Two Small Consensus Regions for Prostate Cancer Genes at 8p
Authors: Chang Bao-li , Liu Wennuan , Sun Jishan , Dimitrov Latchezar , Li Tao , Turner Aubrey R. , Zheng Siqun L. , Isaacs William B. , Xu Jianfeng 
Published: May 2007

Abstract
The evidence for tumor suppressor genes at 8p is well supported by many somatic deletion studies and genetic linkage studies. However, it remains a challenge to pinpoint the tumor suppressor genes at 8p primarily because the implicated regions are broad. In this study, we attempted to narrow down the implicated regions by incorporating evidence from both somatic and germline studies. Using high-resolution Affymetrix arrays, we identified two small common deleted regions among 55 prostate tumors at 8p23.1 (9.8–11.5 Mb) and 8p21.3 (20.6–23.7 Mb). Interestingly, our fine mapping linkage analysis at 8p among 206 hereditary prostate cancer families also provided evidence for linkage at these two regions at 8p23.1 (5.8–11.2 Mb) and at 8p21.3 (19.6–23.9 Mb). More importantly, by combining the results from the somatic deletion analysis and genetic linkage analysis, we were able to further narrow the regions to ∼1.4 Mb at 8p23.1 and ∼3.1 Mb at 8p21.3. These smaller consensus regions may facilitate a more effective search for prostate cancer genes at 8p. [Cancer Res 2007;67(9):4098–103]
A Novel Prodrug of the Green Tea Polyphenol (−)-Epigallocatechin-3-Gallate as a Potential Anticancer Agent
Authors: Landis-Piwowar Kristin R. , Huo Congde , Chen Di , Milacic Vesna , Shi Guoqing , Chan Tak Hang , Dou Q. Ping 
Published: May 2007

Abstract
The most abundant and biologically active green tea catechin, (−)-epigallocatechin-3-gallate or (−)-EGCG, has been shown to act as a proteasome inhibitor and tumor cell death inducer. However, (−)-EGCG is unstable under physiologic conditions and has poor bioavailability. Previously, in an attempt to increase the stability of (−)-EGCG, we introduced peracetate protections to its reactive hydroxyl groups and showed that this peracetate-protected (−)-EGCG [Pro-EGCG (1); formerly named compound 1] could be converted into (−)-EGCG under cell-free conditions. In the current study, we provide evidence that when cultured human breast cancer MDA-MB-231 cells were treated with Pro-EGCG (1), (−)-EGCG was not only converted but also accumulated, accompanied by enhanced levels of proteasome inhibition, growth suppression, and apoptosis induction, compared with cells treated with natural (−)-EGCG. To investigate the potential use of Pro-EGCG (1) as a novel prodrug that converts to a cellular proteasome inhibitor and anticancer agent in vivo, MDA-MB-231 tumors were induced in nude mice, followed by treatment with Pro-EGCG (1) or (−)-EGCG for 31 days. Results of this in vivo study showed a significant inhibition of breast tumor growth by Pro-EGCG (1), compared with (−)-EGCG, associated with increased proteasome inhibition and apoptosis induction in tumor tissues. In conclusion, we have shown that Pro-EGCG (1) increases the bioavailability, stability, and proteasome-inhibitory and anticancer activities of (−)-EGCG in human breast cancer cells and tumors, suggesting its potential use for cancer prevention and treatment. [Cancer Res 2007;67(9):4303–10]
Phosphorylation and Activation of Cell Division Cycle Associated 8 by Aurora Kinase B Plays a Significant Role in Human Lung Carcinogenesis
Authors: Hayama Satoshi , Daigo Yataro , Yamabuki Takumi , Hirata Daizaburo , Kato Tatsuya , Miyamoto Masaki , Ito Tomoo , Tsuchiya Eiju , Kondo Satoshi , Nakamura Yusuke 
Published: May 2007

Abstract
Through genome-wide gene expression analysis of lung carcinomas, we detected in the great majority of lung cancer samples cotransactivation of cell division cycle associated 8 (CDCA8) and aurora kinase B (AURKB), which were considered to be components of the vertebrate chromosomal passenger complex. Immunohistochemical analysis of lung cancer tissue microarrays showed that overexpression of CDCA8 and AURKB was significantly associated with poor prognosis of lung cancer patients. AURKB directly phosphorylated CDCA8 at Ser154, Ser219, Ser275, and Thr278 and seemed to stabilize CDCA8 protein in cancer cells. Suppression of CDCA8 expression with small interfering RNA against CDCA8 significantly suppressed the growth of lung cancer cells. In addition, functional inhibition of interaction between CDCA8 and AURKB by a cell-permeable peptide corresponding to 20-amino acid sequence of a part of CDCA8 (11R-CDCA8261–280), which included two phosphorylation sites by AURKB, significantly reduced phosphorylation of CDCA8 and resulted in growth suppression of lung cancer cells. Our data imply that selective suppression of the CDCA8-AURKB pathway could be a promising therapeutic strategy for treatment of lung cancer patients. [Cancer Res 2007;67(9):4113–22]
Preclinical Evaluation of EC145, a Folate-Vinca Alkaloid Conjugate
Authors: Reddy Joseph A. , Dorton Ryan , Westrick Elaine , Dawson Alicia , Smith Terri , Xu Le-Cun , Vetzel Marilynn , Kleindl Paul , Vlahov Iontcho R. , Leamon Christopher P. 
Published: May 2007

Abstract
We recently developed a new group of folate-conjugated Vinca alkaloids, one of which, EC145, emerged as a candidate for clinical development. Brief treatment of nude mice bearing ∼100 mm3 folate receptor-positive human xenografts led to complete response (CR) in 5/5 mice and cures (i.e., remission without a relapse for &gt;90 days post-tumor implantation) in 4/5 mice. Multiple CRs and cures were also noted when EC145 was used to treat mice initially bearing tumors as large as 750 mm3. Likewise, complete cures (5/5) resulted following the treatment of an aggressive folate receptor–positive J6456 lymphoma model. The activity of EC145 was not accompanied by noticeable weight loss or major organ tissue degeneration. Furthermore, no significant antitumor activity (0/5 CR) was observed in EC145-treated animals that were co-dosed with an excess of a benign folate ligand, thus demonstrating the target-specific activity of EC145. The enhanced therapeutic index due to folate conjugation was also evidenced by the fact that the unconjugated drug (desacetylvinblastine monohydrazide) was found to be completely inactive when administered at nontoxic dose levels and only marginally active when given at highly toxic dose levels. Subsequent dose regimen studies confirmed that EC145 given on a more frequent, qdx5 schedule resulted in the most effective antitumor response as compared with an equivalent total dose given on thrice- or single-injection-per-week schedule. Taken together, these studies show that EC145 has significant antiproliferative activity and tolerability, thus lending support to an ongoing phase 1 trial for the treatment of advanced malignancies. [Cancer Res 2007;67(9):4434–42]
Potential risks of bone marrow cell transplantation into infarcted hearts
Authors: Breitbach Martin , Bostani Toktam , Roell Wilhelm , Xia Ying , Dewald Oliver , Nygren Jens M. , Fries Jochen W. U. , Tiemann Klaus , Bohlen Heribert , Hescheler Juergen , Welz Armin , Bloch Wilhelm , Jacobsen Sten Eirik W. , Fleischmann Bernd K. 
Published: May 2007

Abstract
Cellular replacement therapy has emerged as a novel strategy for the treatment of heart failure. The aim of our study was to determine the fate of injected mesenchymal stem cells (MSCs) and whole bone marrow (BM) cells in the infarcted heart. MSCs were purified from BM of transgenic mice and characterized using flow cytometry and in vitro differentiation assays. Myocardial infarctions were generated in mice and different cell populations including transgenic MSCs, unfractionated BM cells, or purified hematopoietic progenitors were injected. Encapsulated structures were found in the infarcted areas of a large fraction of hearts after injecting MSCs (22 of 43, 51.2%) and unfractionated BM cells (6 of 46, 13.0%). These formations contained calcifications and/or ossifications. In contrast, no pathological abnormalities were found after injection of purified hematopoietic progenitors (0 of 5, 0.0%), fibroblasts (0 of 5, 0.0%), vehicle only (0 of 30, 0.0%), or cytokine-induced mobilization of BM cells (0 of 35, 0.0%). We conclude that the developmental fate of BM-derived cells is not restricted by the surrounding tissue after myocardial infarction and that the MSC fraction underlies the extended bone formation in the infarcted myocardium. These findings seriously question the biologic basis and clinical safety of using whole BM and in particular MSCs to treat nonhematopoietic disorders.
Analysis of probe level patterns in Affymetrix microarray data
Authors: Cambon Alexander C , Khalyfa Abdelnaby , Cooper Nigel GF , Thompson Caryn M 
Published: May 2007

AbstractBackgroundMicroarrays have been used extensively to analyze the expression profiles for thousands of genes in parallel. Most of the widely used methods for analyzing Affymetrix Genechip microarray data, including RMA, GCRMA and Model Based Expression Index (MBEI), summarize probe signal intensity data to generate a single measure of expression for each transcript on the array. In contrast, other methods are applied directly to probe intensities, negating the need for a summarization step.ResultsIn this study, we used the Affymetrix rat genome Genechip to explore variability in probe response patterns within transcripts. We considered a number of possible sources of variability in probe sets including probe location within the transcript, middle base pair of the probe sequence, probe overlap, sequence homology and affinity. Although affinity, middle base pair and probe location effects may be seen at the gross array level, these factors only account for a small proportion of the variation observed at the gene level. A BLAST search and the presence of probe by treatment interactions for selected differentially expressed genes showed high sequence homology for many probes to non-target genes.ConclusionWe suggest that examination and modeling of probe level intensities can be used to guide researchers in refining their conclusions regarding differentially expressed genes. We discuss implications for probe sequence selection for confirmatory analysis using real time PCR.
MRX87 family with Aristaless Xdup24bp mutation and implication for polyAlanine expansions
Authors: Laperuta Carmela , Spizzichino Letizia , D'Adamo Pio , Monfregola Jlenia , Maiorino Antonio , D'Eustacchio Angela , Ventruto Valerio , Neri Giovanni , D'Urso Michele , Chiurazzi Pietro , Ursini Matilde Valeria , Miano Maria Giuseppina 
Published: May 2007

Abstract

Background
Cognitive impairments are heterogeneous conditions, and it is estimated that 10% may be caused by a defect of mental function genes on the X chromosome. One of those genes is Aristaless related homeobox (ARX) encoding a polyA-rich homeobox transcription factor essential for cerebral patterning and its mutations cause different neurologic disorders. We reported on the clinical and genetic analysis of an Italian family with X-linked mental retardation (XLMR) and intra-familial heterogeneity, and provided insight into its molecular defect.

Methods
We carried out on linkage-candidate gene studies in a new MRX family (MRX87). All coding regions and exon-intron boundaries of ARX gene were analysed by direct sequencing.

Results
MRX87 patients had moderate to profound cognition impairment and a combination of minor congenital anomalies. The disease locus, MRX87, was mapped between DXS7104 and DXS1214, placing it in Xp22-p21 interval, a hot spot region for mental handicap. An in frame duplication of 24 bp (ARXdup24) in the second polyAlanine tract (polyA_II) in ARX was identified.

Conclusion
Our study underlines the role of ARXdup24 as a critical mutational site causing mental retardation linked to Xp22. Phenotypic heterogeneity of MRX87 patients represents a new observation relevant to the functional consequences of polyAlanine expansions enriching the puzzling complexity of ARXdup24-linked diseases.
The importance of a taste. A comparative study on wild food plant consumption in twenty-one local communities in Italy
Authors: Ghirardini Maria Pia , Carli Marco , del Vecchio Nicola , Rovati Ariele , Cova Ottavia , Valigi Francesco , Agnetti Gaia , Macconi Martina , Adamo Daniela , Traina Mario , Laudini Francesco , Marcheselli Ilaria , Caruso Nicolò , Gedda Tiziano , Donati Fabio , Marzadro Alessandro , Russi Paola , Spaggiari Caterina , Bianco Marcella , Binda Riccardo , Barattieri Elisa , Tognacci Alice , Girardo Martina , Vaschetti Luca , Caprino Piero , Sesti Erika , Andreozzi Giorgia , Coletto Erika , Belzer Gabriele , Pieroni Andrea 
Published: May 2007

Abstract
A comparative food ethnobotanical study was carried out in twenty-one local communities in Italy, fourteen of which were located in Northern Italy, one in Central Italy, one in Sardinia, and four in Southern Italy. 549 informants were asked to name and describe food uses of wild botanicals they currently gather and consume. Data showed that gathering, processing and consuming wild food plants are still important activities in all the selected areas. A few botanicals were quoted and cited in multiple areas, demonstrating that there are ethnobotanical contact points among the various Italian regions (Asparagus acutifolius, Reichardia picroides, Cichorium intybus, Foeniculum vulgare, Sambucus nigra, Silene vulgaris, Taraxacum officinale, Urtica dioica, Sonchus and Valerianella spp.). One taxon (Borago officinalis) in particular was found to be among the most quoted taxa in both the Southern and the Northern Italian sites.
However, when we took into account data regarding the fifteen most quoted taxa in each site and compared and statistically analysed these, we observed that there were a few differences in the gathering and consumption of wild food plants between Northern and Southern Italy. In the North, Rosaceae species prevailed, whereas in the South, taxa belonging to the Asteraceae, Brassicaceae, and Liliaceae s.l. families were most frequently cited. We proposed the hypothesis that these differences may be due to the likelihood that in Southern Italy the erosion of TK on wild vegetables is taking place more slowly, and also to the likelihood that Southern Italians' have a higher appreciation of wild vegetables that have a strong and bitter taste.
A correspondence analysis confirmed that the differences in the frequencies of quotation of wild plants within the Northern and the Southern Italian sites could be ascribed only partially to ethnic/cultural issues. An additional factor could be recent socio-economic shifts, which may be having a continued effort on people's knowledge of wild food plants and the way they use them.
Finally, after having compared the collected data with the most important international and national food ethnobotanical databases that focus on wild edible plants, we pointed out a few uncommon plant food uses (e.g. Celtis aetnensis fruits, Cicerbita alpine shoots, Helichrysum italicum leaves, Lonicera caprifolium fruits, Symphytum officinale leaves), which are new, or have thus far been recorded only rarely.
A search engine to identify pathway genes from expression data on multiple organisms
Authors: Chen Chunnuan , Weirauch Matthew T , Powell Corey C , Zambon Alexander C , Stuart Joshua M 
Published: May 2007

AbstractBackgroundThe completion of several genome projects showed that most genes have not yet been characterized, especially in multicellular organisms. Although most genes have unknown functions, a large collection of data is available describing their transcriptional activities under many different experimental conditions. In many cases, the coregulatation of a set of genes across a set of conditions can be used to infer roles for genes of unknown function.ResultsWe developed a search engine, the Multiple-Species Gene Recommender (MSGR), which scans gene expression datasets from multiple organisms to identify genes that participate in a genetic pathway. The MSGR takes a query consisting of a list of genes that function together in a genetic pathway from one of six organisms:Homo sapiens,Drosophila melanogaster,Caenorhabditis elegans,Saccharomyces cerevisiae,Arabidopsis thaliana, andHelicobacter pylori. Using a probabilistic method to merge searches, the MSGR identifies genes that are significantly coregulated with the query genes in one or more of those organisms. The MSGR achieves its highest accuracy for many human pathways when searches are combined across species. We describe specific examples in which new genes were identified to be involved in a neuromuscular signaling pathway and a cell-adhesion pathway.ConclusionThe search engine can scan large collections of gene expression data for new genes that are significantly coregulated with a pathway of interest. By integrating searches across organisms, the MSGR can identify pathway members whose coregulation is either ancient or newly evolved.
Online Auction and List Price Revenue Management
Authors: Caldentey René , Vulcano Gustavo 
Published: May 2007

We analyze a revenue management problem in which a seller facing a Poisson arrival stream of consumers operates an online multiunit auction. Consumers can get the product from an alternative list price channel. We consider two variants of this problem: In the first variant, the list price is an external channel run by another firm. In the second one, the seller manages both the auction and the list price channels. Each consumer, trying to maximize his own surplus, must decide either to buy at the posted price and get the item at no risk, or to join the auction and wait until its end, when the winners are revealed and the auction price is disclosed. Our approach consists of two parts. First, we study structural properties of the problem, and show that the equilibrium strategy for both versions of this game is of the threshold type, meaning that a consumer will join the auction only if his arrival time is above a function of his own valuation. This consumer’s strategy can be computed using an iterative algorithm in a function space, provably convergent under some conditions. Unfortunately, this procedure is computationally intensive. Second, and to overcome this limitation, we formulate an asymptotic version of the problem, in which the demand rate and the initial number of units grow proportionally large. We obtain a simple closed-form expression for the equilibrium strategy in this regime, which is then used as an approximate solution to the original problem. Numerical computations show that this heuristic is very accurate. The asymptotic solution culminates in simple and precise recipes of how bidders should behave, as well as how the seller should structure the auction, and price the product in the dual-channel case.
Intertemporal Pricing with Strategic Customer Behavior
Authors: Su Xuanming 
Published: May 2007

This paper develops a model of dynamic pricing with endogenous intertemporal demand. In the model, there is a monopolist who sells a finite inventory over a finite time horizon. The seller adjusts prices dynamically to maximize revenue. Customers arrive continually over the duration of the selling season. At each point in time, customers may purchase the product at current prices, remain in the market at a cost to purchase later, or exit, and they wish to maximize individual utility. The customer population is heterogeneous along two dimensions: they may have different valuations for the product and different degrees of patience (waiting costs).We demonstrate that heterogeneity in both valuation and patience is important because they jointly determine the structure of optimal pricing policies. In particular, when high-value customers are proportionately less patient, markdown pricing policies are effective because the high-value customers would buy early at high prices while the low-value customers are willing to wait (i.e., they are not lost). On the other hand, when the high-value customers are more patient than the low-value customers, prices should increase over time to discourage inefficient waiting. Contrary to intuition, we find that strategic waiting by customers may sometimes benefit the seller: when low-value customers wait, they compete for availability with high-value customers and thus increase their willingness to pay. Our results also shed light on how the composition of the customer population affects optimal revenue, consumer surplus, and social welfare. Finally, we consider the long-run problem of selecting the optimal initial stocking quantity.
Twin Research, and its Multiple Births and Expressions: A Short, Personal Voyage Through its Scope, History,and Organization
Authors: Parisi Paolo 
Published: May 2007

AbstractThe notion of twins and twinning involves a multiplicity of meanings and contexts that altogether encompass an unexpectedly wide and significant part of human experience, culture, and endeavor. This cultural polysemy is, to some extent, also an attribute of twin research, which has structured itself around a multiplicity of scientific areas of enquiry, and across time, throughout a multiplicity of births and rebirths, periodically declining and resurging as a phoenix from its ashes. What is proposed is a short voyage through this polysemy and phoenixity of twinning and twin research, and through the structuring process that has accompanied its developments, international scope, and organization. No claim to completeness, but an attempt to dig into personal memory and experience, and share some recollections of the main steps of the process, and particularly the evolution of the journal, the society, the international meetings, and their role in supporting the area's persistence and continuous revivals and adaptations until today.
Choice of Residential Location: Chance, Family Influences, or Genes?
Authors: Whitfield John B. , Zhu Gu , Heath Andrew C. , Martin Nicholas G. 
Published: May 2007

AbstractThe choice of where to live would appear to be determined by a combination of economic constraints and personal preferences. We have tested how far this choice is affected by the continuing effects of the environment shared within families, and genetic variation between people, using data from twin studies conducted in Australia. The addresses provided by study participants were categorized as urban, suburban and nonurban, and data were analyzed in three adult age groups. There were significant effects of both shared environment and genes, and the balance between them was affected by both sex and age. Shared environment accounted for some 50% of variation in the youngest group, but only about 10% in the oldest. As shared environmental effects decreased, additive genetic effects increased. These results have implications for internal migration of people within countries and, over the long term, for gene flow within and between populations. They may also be pertinent to the different prevalences of certain psychiatric diseases between city and country locations. Comparisons between countries with different demography are needed to confirm and further characterize these effects.