bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention
Authors: Cavallo Federica , Astolfi Annalisa , Iezzi Manuela , Cordero Francesca , Lollini Pier-Luigi , Forni Guido , Calogero Raffaele 
Published: December 2005

AbstractBackgroundNeoplastic transformation is a multistep process in which distinct gene products of specific cell regulatory pathways are involved at each stage. Identification of overexpressed genes provides an unprecedented opportunity to address the immune system against antigens typical of defined stages of neoplastic transformation. HER-2/neu/ERBB2 (Her2) oncogene is a prototype of deregulated oncogenic protein kinase membrane receptors. Mice transgenic for rat Her2 (BALB-neuT mice) were studied to evaluate the stage in which vaccines can prevent the onset of Her2 driven mammary carcinomas. As Her2 is not overexpressed in all mammary carcinomas, definition of an additional set of tumor associated antigens (TAAs) expressed at defined stages by most breast carcinomas would allow a broader coverage of vaccination. To address this question, a meta-analysis was performed on two transcription profile studies [1, 2] to identify a set of new TAA targets to be used instead of or in conjunction with Her2.ResultsThe five TAAs identified (Tes, Rcn2, Rnf4, Cradd, Galnt3) are those whose expression is linearly related to the tumor mass increase in BALB-neuT mammary glands. Moreover, they have a low expression in normal tissues and are generally expressed in human breast tumors, though at a lower level than Her2.ConclusionAlthough the number of putative TAAs identified is limited, this pilot study suggests that meta-analysis of expression profiles produces results that could assist in the designing of pre-clinical immunopreventive vaccines.
Secondary structure assignment that accurately reflects physical and evolutionary characteristics
Authors: Cubellis Maria Vittoria , Cailliez Fabien , Lovell Simon C 
Published: December 2005

Abstract

Background
Secondary structure is used in hierarchical classification of protein structures, identification of protein features, such as helix caps and loops, for fold recognition, and as a precursor to ab initio structure prediction. There are several methods available for assigning secondary structure if the three-dimensional structure of the protein is known. Unfortunately they differ in their definitions, particularly in the exact positions of the termini. Additionally, most existing methods rely on hydrogen bonding, which means that important secondary structural classes, such as isolated β-strands and poly-proline helices cannot be identified as they do not have characteristic hydrogen-bonding patterns. For this reason we have developed a more accurate method for assigning secondary structure based on main chain geometry, which also allows a more comprehensive assignment of secondary structure.

Results
We define secondary structure based on a number of geometric parameters. Helices are defined based on whether they fit inside an imaginary cylinder: residues must be within the correct radius of a central axis. Different types of helices (alpha, 310 or π) are assigned on the basis of the angle between successive peptide bonds. β-strands are assigned based on backbone dihedrals and with alternating peptide bonds. Thus hydrogen bonding is not required and β-strands can be within a parallel sheet, antiparallel sheet, or can be isolated. Poly-proline helices are defined similarly, although with three-fold symmetry.

Conclusion
We find that our method better assigns secondary structure than existing methods. Specifically, we find that comparing our methods with those of others, amino-acid trends at helix caps are stronger, secondary structural elements less likely to be concatenated together and secondary structure guided sequence alignment is improved. We conclude, therefore, that secondary structure assignments using our method better reflects physical and evolutionary characteristics of proteins.
The program is available from http://www.bioinf.man.ac.uk/~lovell/segno.shtml
ParPEST: a pipeline for EST data analysis based on parallel computing
Authors: D'Agostino Nunzio , Aversano Mario , Chiusano Maria Luisa 
Published: December 2005

Abstract

Background
Expressed Sequence Tags (ESTs) are short and error-prone DNA sequences generated from the 5' and 3' ends of randomly selected cDNA clones. They provide an important resource for comparative and functional genomic studies and, moreover, represent a reliable information for the annotation of genomic sequences. Because of the advances in biotechnologies, ESTs are daily determined in the form of large datasets. Therefore, suitable and efficient bioinformatic approaches are necessary to organize data related information content for further investigations.

Results
We implemented ParPEST (Par allel P rocessing of EST s), a pipeline based on parallel computing for EST analysis. The results are organized in a suitable data warehouse to provide a starting point to mine expressed sequence datasets. The collected information is useful for investigations on data quality and on data information content, enriched also by a preliminary functional annotation.

Conclusion
The pipeline presented here has been developed to perform an exhaustive and reliable analysis on EST data and to provide a curated set of information based on a relational database. Moreover, it is designed to reduce execution time of the specific steps required for a complete analysis using distributed processes and parallelized software. It is conceived to run on low requiring hardware components, to fulfill increasing demand, typical of the data used, and scalability at affordable costs.
Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos
Authors: Goossens Karen , Van Poucke Mario , Van Soom Ann , Vandesompele Jo , Van Zeveren Alex , Peelman Luc J 
Published: December 2005

Abstract

Background
Real-time quantitative PCR is a sensitive and very efficient technique to examine gene transcription patterns in preimplantation embryos, in order to gain information about embryo development and to optimize assisted reproductive technologies. Critical to the succesful application of real-time PCR is careful assay design, reaction optimization and validation to maximize sensitivity and accuracy. In most of the studies published GAPD, ACTB or 18S rRNA have been used as a single reference gene without prior verification of their expression stability. Normalization of the data using unstable controls can result in erroneous conclusions, especially when only one reference gene is used.

Results
In this study the transcription levels of 8 commonly used reference genes (ACTB, GAPD, Histone H2A, TBP, HPRT1, SDHA, YWHAZ and 18S rRNA) were determined at different preimplantation stages (2-cell, 8-cell, blastocyst and hatched blastocyst) in order to select the most stable genes to normalize quantitative data within different preimplantation embryo stages.

Conclusion
Using the geNorm application YWHAZ, GAPD and SDHA were found to be the most stable genes across the examined embryonic stages, while the commonly used ACTB was shown to be highly regulated. We recommend the use of the geometric mean of those 3 reference genes as an accurate normalization factor, which allows small expression differences to be reliably measured.
Neogenin expression may be inversely correlated to the tumorigenicity of human breast cancer
Authors: Lee Jeong Eon , Kim Hee Joung , Bae Ji Yeon , Kim Seok Won , Park Joon-Suk , Shin Hyuk Jai , Han Wonshik , Kim Sung-Won , Kang Kyung-Sun , Noh Dong-Young 
Published: December 2005

Abstract

Background
Neogenin is expressed in cap cells that have been suggested to be mammary stem or precursor cells. Neogenin is known to play an important role in mammary morphogenesis; however its relationship to tumorigenesis remains to be elucidated.

Methods
To compare the expression levels of neogenin in cells with different tumorigenicity, the expression levels in M13SV1, M13SV1R2 and M13SV1R2N1 cells, which are immortalized derivatives of type I human breast epithelial cells, were evaluated. Then we measured the expression level of neogenin in paired normal and cancer tissues from eight breast cancer patients. Tissue array analysis was performed for 54 human breast tissue samples with different histology, and the results were divided into four categories (none, weak, moderate, strong) by a single well-trained blinded pathologist and statistically analyzed.

Results
The nontumorigenic M13SV1 cells and normal tissues showed stronger expression of neogenin than the M13SV1R2N1 cells and the paired cancer tissues. In the tissue array, all (8/8) of the normal breast tissues showed strong neogenin expression, while 93.5% (43/46) of breast cancer tissues had either no expression or only moderate levels of neogenin expression. There was a significant difference, in the expression level of neogenin, in comparisons between normal and infiltrating ductal carcinoma (p < 0.001).

Conclusion
Neogenin may play a role in mammary carcinogenesis as well as morphogenesis, and the expression may be inversely correlated with mammary carcinogenicity. The value of neogenin as a potential prognostic factor needs further evaluation.
The transcriptome of Toxoplasma gondii
Authors: Radke Jay R , Behnke Michael S , Mackey Aaron J , Radke Josh B , Roos David S , White Michael W 
Published: December 2005

AbstractBackgroundToxoplasma gondiigives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown.ResultsWe have used serial analysis of gene expression (SAGE) to define theToxoplasma gondiitranscriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags) representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity.ConclusionThis study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found thatToxoplasmamRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across allToxoplasmachromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and expression levels of mRNAs in primary populations (Day-6 post-sporozoite infection) that occur prior to the onset of bradyzoite development that were uniquely shared with the virulent Type I-RH laboratory strain suggesting that development of RH may be arrested. By contrast, strains from Type II-Me49B7 and Type III-VEGmsj contain SAGE tags corresponding to bradyzoite genes, which suggests that priming of developmental expression likely plays a role in the greater capacity of these strains to complete bradyzoite development.
Clinical Cancer Advances 2005: Major Research Advances in Cancer Treatment, Prevention, and Screening—A Report From the American Society of Clinical Oncology
Authors: Herbst Roy S. , Bajorin Dean F. , Bleiberg Harry , Blum Diane , Hao Desirée , Johnson Bruce E. , Ozols Robert F. , Demetri George D. , Ganz Patricia A. , Kris Mark G. , Levin Bernard , Markman Maurie , Raghavan Derek , Reaman Gregory H. , Sawaya Raymond , Schuchter Lynn M. , Sweetenham John W. , Vahdat Linda T. , Vokes Everett E. , Winn Rodger J. , Mayer Robert J. 
Published: December 2005

A MESSAGE FROM ASCO’s PRESIDENT This year, for the first time, the American Society of Clinical Oncology (ASCO) is publishing Clinical Cancer Advances 2005: Major Research Advances in Cancer Treatment, Prevention, and Screening, an annual review of the most significant clinical research presented or published over the past year across all cancer types. ASCO embarked on this project to provide the public, patients, policymakers, and physicians with an accessible summary of the year's most important research advances. While not intended to serve as a comprehensive review, this report provides a year-end snapshot of research that will have the greatest impact on patient care. As you will read, there is much good news from the front lines of cancer research. These pages report on new chemotherapy regimens that sharply reduce the risk of recurrence for very common cancers; the “coming of age” of targeted cancer therapies; promising studies of drugs to prevent cancer; and improvements in quality of life for people living with the disease, among many other advances. Survival rates for cancer are on the rise, increasing from 50% to 64% over the last 30 years. Cancer still exacts an enormous toll, however. Nearly 1.4 million Americans will be diagnosed this year, and some 570,000 will die of the disease. Clearly, more research is needed to find effective therapies for the most stubborn cancer types and stages. We need to know more about the long-term effects of newer, more targeted cancer therapies, some of which need to be taken over long periods of time. And we need to devote far greater attention to tracking and improving the care of the nearly 10 million cancer survivors in the United States today. Despite these and other challenges, the message of this report is one of hope. Through the dedicated, persistent pursuit of clinical research and participation in clinical trials by people with cancer, we steadily uncover new and better ways of treating, diagnosing, and preventing a disease that touches the lives of so many. I want to thank the Editorial Board members, the Specialty Editors, and the ASCO Cancer Communications Committee for their dedicated work to develop this report, and I hope you find it useful. Sincerely, Sandra J. Horning, MD President American Society of Clinical Oncology
Prophylactic Fluconazole Is Effective in Preventing Fungal Colonization and Fungal Systemic Infections in Preterm Neonates: A Single-Center, 6-Year, Retrospective Cohort Study
Authors: Manzoni Paolo , Arisio Riccardo , Mostert Michael , Leonessa MariaLisa , Farina Daniele , Latino Maria Agnese , Gomirato Giovanna 
Published: December 2005

OBJECTIVE. Despite the promising preliminary results observed in extremely low birth weight (ELBW) populations, the use of fluconazole to prevent fungal colonization and infection in preterm neonates in the NICU is still an open question and not yet recommended as a standard of care. We have reviewed our 6-year series to assess the effectiveness and safety of this form of prophylaxis.METHODS. This retrospective study consisted of 465 neonates who weighed &lt;1500 g at birth and were admitted to our NICU in the period 1998–2003. Those who were born between 1998 and 2000 and did not receive fluconazole prophylaxis (group A, n = 240) were compared with those who were born between 2001 and 2003 and treated with fluconazole until the 30th day of life (45th for neonates &lt;1000 g at birth; group B, n = 225). Weekly surveillance cultures were obtained from all patients. Incidence of fungal colonization, incidence of systemic fungal infection (SFI), rate of progression from colonization to infection, and mortality rates attributable to fungi were calculated for both groups and separately for neonates who were &lt;1000 g (ELBW) and were 1001 to 1500 g (NE-VLBW) at birth.RESULTS. Overall fungal colonization was significantly lower in group B (24.0%) than in group A (43.8%; relative risk [RR]: 0.406; 95% confidence interval [CI]: 0.273–0.605). The same was true of neonates with colonization in multiple sites (2.6% vs 5.8%) and of those with colonization from high-risk sites (5.8% vs 19.2%). SFI incidence was significantly lower in group B (10 of 225 cases; 4.4%) than in group A (40 of 240 cases; 16.7%; RR: 0.233; 95% CI: 0.113–0.447). Reduction of both colonization and SFI in group B was greater in the ELBW neonates and also significant in the NE-VLBW neonates. Rate of progression from colonization to infection was significantly lower in group B (0.17 vs 0.38; RR: 0.369; 95% CI: 0.159–0.815). Crude mortality rate attributable to Candida species was 1.7% (4 of 240) in group A vs 0% (0 of 225) in group B. Overall mortality rate (any cause before hospital discharge) was similar in the two groups (11.2% vs 10.6%), but in colonized infants (n = 159), it was significantly lower in group B (3.7% vs 18.1%; RR: 0.174; 95% CI: 0.039–0.778). The incidence of natively fluconazole-resistant fungal species did not increase over the years, and patterns of sensitivity to fluconazole remained the same. No adverse reaction related to fluconazole occurred.CONCLUSIONS. Prophylactic fluconazole significantly reduces the incidence of colonization and systemic infection by Candida species in both ELBW and NE-VLBW neonates and decreases the rates of progression from initial colonization to massive colonization and to systemic infection. All VLBW neonates may benefit from fluconazole prophylaxis.
Spatial Distribution of Microbial 2,4‐Dichlorophenoxy Acetic Acid Mineralization from Field to Microhabitat Scales
Authors: Vieublé Gonod Laure , Chadoeuf Joël , Chenu Claire 
Published: December 2005

Little is known about spatial variability of microbial activity, particularly at microscales. This is especially true for the fate and degradation of pesticides. The objective was to sample soil from micro to field scales and apply geostatistics on the potential mineralization of a widely used herbicide 2,4‐dichlorophenoxy acetic acid (2,4‐D; C8H6Cl2O3). Soil cores were sampled in the plow layer of a cultivated soil with a systematic sampling procedure. In a first experiment 2,4‐D mineralization was measured on 39 crushed cores and we analyzed variability of mineralization at the field scale, from decameter to meter and from meter to decimeter scale. In a second experiment, 432 soil cubes (about 216 mm3) were used to study the variability of mineralization at the “microhabitat” scale from meter to millimeter. The spatial dependence of 2,4‐D mineralization was first quantified by computing an empirical variogram function. Spatial independence was then tested by comparing the empirical variogram function to its individual confidence bounds at 95% level obtained under independence assumption by a Monte‐Carlo Method.The potential for 2,4‐D mineralization was spatially heterogeneous from field to microhabitat. Mineralization variability increased when the scale decreased from field to microhabitats.Specifically, the coefficient of variability (CV) of 2,4‐D mineralization was of 18.5% at the field scale, 7–22% at the meter scale, 47.9% at the inter‐cores scale, and 25–160% at the intra‐core scale (microhabitat scale). 2,4‐D mineralization was spatially structured only at the microhabitat scale (hot spots). This variability at fine scales should be considered when sampling soil processes involving microbial activities.
Pyridine and Pyridine Derivatives
Authors: Scriven Eric F. V. , Murugan Ramiah 
Published: December 2005

AbstractCommercial manufacture, industrial chemistry, and market uses of pyridine and pyridine compounds are reviewed. Pyridines often serve as intermediates for manufacture of products that are bioactive, such as medicinals, herbicides, insecticides, and fungicides. Significant end products for these market applications are identified. Important physical properties are also listed. Discussion of manufacture includes raw materials used, energy utilization, economics, toxicity of compounds, and safety factors.
Tin and Tin Alloys
Authors: Gaver Charles C. ,   Updated by Staff
Published: December 2005

Abstract
Tin is one of the world’s most ancient metals. In most cases, tin is used on or in a manufactured material in small amounts, much out of proportion to the purpose it serves. Tin in some form has been associated with the economic and cultural growth of civilization. Food preservation and canning developed rapidly with the invention of tin‐coated steel; transportation and high speed machinery became a reality with the invention of tin‐base bearing metals; the casting of type metal was an important advance in printing technology; bronze alloys became weapons, tools, and architectural objects; and telecommunications and electronic equipment depend on the tin‐lead soldered joint. New solders are expected to be lead‐free. In modern technology, uses of tin include the plating of protective coatings, nuclear energy, plastics and other polymers, agriculture, biochemistry, electronic packaging, and glassmaking. Physical properties, chemical properties, processing, economic aspects, specifications and analytical methods, health and safety factors, and uses of tin are discussed.
Synthesis of 2‐Haloalkylpyridines via Cp*RuCl‐Catalyzed Cycloaddition of 1,6‐Diynes with α‐Halonitriles. Unusual Halide Effect in Catalytic Cyclocotrimerization
Authors: Yamamoto Yoshihiko , Kinpara Keisuke , Nishiyama Hisao , Itoh Kenji 
Published: December 2005

AbstractIn the presence of 2–5 mol % Cp*RuCl (cod), various 1,6‐diynes reacted with α‐monohalo‐ and α,α‐dihalonitriles at ambient temperature to afford 2‐haloalkylpyridines in 42–93% isolated yields. The failure of acetonitrile, N,N‐dimethylaminoacetonitrile, phenylthioacetonitrile, and methyl cyanoacetate as nitrile substrate clearly showed that the α halogen substitution is essential for the present cycloaddition under mild conditions. The cycloaddition of unsymmetrical diynes bearing a substituent on one alkyne terminal gave 2,3,4,6‐substituted pyridines exclusively.
Stability of protease in organic solvent: Structural identification by solid‐state NMR of lyophilized papain before and after 1‐propanol treatment and the corresponding enzymatic activities
Authors: Matsubara Teruhiko , Fujita Risa , Sugiyama Shigeru , Kawashiro Katsuhiro 
Published: December 2005

AbstractLyophilized enzyme powder is often used in organic solvents. However, the enzymatic activity decreases during the reaction process. In the present study, the relation between structural stability and enzymatic activity in an organic solvent was investigated. 13C cross‐polarization magic angle spinning NMR spectroscopy was used to determine the secondary structure of lyophilized papain in the solid‐state. Deconvolution of the peaks of the backbone carbonyl carbons suggested that the proportion of β‐sheet conformation increased after lyophilization from a phosphate buffer solution. The esterification of N‐benzyloxycarbonyl phenylalanylalanine amide was attempted using the lyophilized papain as a catalyst in anhydrous 1‐propanol. The yield of ester was 46.1% after 48 h at 50°C, but this reaction slowed remarkably after 48 h. When the lyophilized papain was suspended in anhydrous 1‐propanol for 7 days without the substrate, the proportion of β‐sheet conformation was further increased and the suspended papain had no activity. These results suggest that the increase in β‐sheet conformation caused inactivation of papain. The increase in β‐sheet conformation caused by both lyophilization and suspension in propanol was found, which was related to a decrease in enzymatic activity. © 2005 Wiley Periodicals, Inc.