bluuebunny/crossref_metadata_2025_split huggingface dataset:
CHALK AND FLUID INOCULATION METHODS IN STUDYING THE PERCENT RECOVERY OF CLOSTRIDIUM PERFRINGENS, ESCHERICHIA COLI AND ENTEROCOCCUS FAECALIS FROM RAW GROUND BEEF
Authors: OBAIDAT MOHAMMAD M. , FUNG DANIEL Y.C. 
Published: December 2005

ABSTRACT The fluid inoculation method is widely used in studying the growth characteristics and percent recovery of microorganisms in food. In addition to this method a new method, called the chalk method, was introduced and has been successfully used. This research aimed to compare the percent recovery of Clostridium perfringens, Escherichia coli and Enterococcus faecalis from raw ground beef using the chalk and fluid inoculation methods. It also aimed to compare the chalk and fluid methods in studying the percent recovery of the three microorganisms. The results show that the percent recoveries of C. perfringens, E. coli, and E. faecalis were significantly different (P < 0.05) using the two inoculation methods, except for the percent recovery of C. perfringens and E. coli using the fluid method (P > 0.05). The percent recovery using chalk powder inoculum was significantly lower (P < 0.05) than the percent recovery using fluid inoculum for E. coli and E. faecalis. The results also show that E. faecalis has the highest percent recovery using both methods, and E. coli has the lowest using the chalk method. It can be concluded that chalk inoculation is better than fluid inoculation because it gives better percent recovery, saves time, is easier to perform, is more precise, and gives information about inoculum distribution.
Phenotypic Modulation of Intima and Media Smooth Muscle Cells in Fatal Cases of Coronary Artery Lesion
Authors: Hao Hiroyuki , Gabbiani Giulio , Camenzind Edoardo , Bacchetta Marc , Virmani Renu , Bochaton-Piallat Marie-Luce 
Published: December 2005

Objectives—Characterize the phenotypic features of media and intima coronary artery smooth muscle cells (SMCs) in mildly stenotic plaques, erosions, stable plaques, and in-stent restenosis.Methods and Results—Expression of α-smooth muscle actin (α-SMA), smooth muscle myosin heavy chains (SMMHCs), and smoothelin was investigated by immunohistochemistry followed by morphometric quantification. The cross-sectional area and the expression of cytoskeletal proteins in the media were lower in restenotic lesions and, to a lesser extent, in stable plaques compared with mildly stenotic plaques and erosions. An important expression of α-SMA was detected in the intima of the different lesions; moreover, α-SMA staining was significantly larger in erosions compared with all other conditions. In the same location, a striking decrease of SMMHCs and a disappearance of smoothelin were observed in all situations.Conclusions—Medial atrophy is prevalent in restenotic lesions and stable plaques compared with mildly stenotic plaques and erosions. Intimal SMCs of all situations exhibit a phenotypic profile, suggesting that they have modulated into myofibroblasts (MFs). The high accumulation of α-SMA–positive MFs in erosions compared with stable plaques correlates with the higher appearance of thrombotic complications in this situation.
Global Trade and Technology Regimes: The South's Asymmetrical Struggle
Authors: Patterson Rubin 
Published: December 2005

AbstractThe trade and technology regimes of WTO and TRIPS embody the values, objectives, and operational dynamics that primarily satisfy Western powers. Southern states submit to these constraining regimes only to the extent of avoiding severe penalties. They feign compliance whenever possible through "stealthy noncompliance" in order to advance their development and security. This paper addresses three issues: the West-South asymmetrical struggle over technology and trade; the role of state-supported technological development in the South; and the prospective consequences for the South relating to the restricted labor-absorbing capacity of twenty-first century technology.
Globalization and the Requirements of "Good" Environmental Governance
Authors: Bernstein Steven 
Published: December 2005

AbstractA growing number of regulations and agencies dealing with the global environment directly affect citizens' lives. In these conditions, a conventional division between international and domestic issues, and between normative and explanatory theory, becomes less tenable, raising corresponding issues of legitimacy, community, and ethics. This chapter assesses liberal environmentalism in terms of a normative theory that considers requirements of authority, epistemic validity, good practices, and practical reason. Despite improvements in terms of efficiency and legitimacy, serious concerns remain concerning the foundations of "good" environmental governance.
Humanitarian Intervention and the Question of Sovereignty: The Case of ASEAN
Authors: Narine Shaun 
Published: December 2005

AbstractThe Association of Southeast Asian Nations (ASEAN) has thrived as a regional institution that defends the traditional understanding of Westphalian sovereignty. In the post-Cold War era, however, pressure from within the international community to redefine sovereignty to accommodate humanitarian intervention has placed ASEAN in a difficult position. Historically, ASEAN has actively opposed the idea of humanitarian intervention. However, the ASEAN states have had to acknowledge that such a norm is emerging within the international society. Moreover, ASEAN's inconsistent defense of its professed values, particularly its reaction to the US invasion of Iraq, has undermined ASEAN's ability to defend the traditional definition of sovereignty.
SNP-VISTA: An interactive SNP visualization tool
Authors: Shah Nameeta , Teplitsky Michael V , Minovitsky Simon , Pennacchio Len A , Hugenholtz Philip , Hamann Bernd , Dubchak Inna L 
Published: December 2005

Abstract
Background
Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at http://genome.lbl.gov/vista/snpvista[1].

Results
We have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable.

Conclusion
The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user.
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments
Authors: Novikov Eugene , Barillot Emmanuel 
Published: December 2005

Abstract
Background
Although DNA microarray technologies are very powerful for the simultaneous quantitative characterization of thousands of genes, the quality of the obtained experimental data is often far from ideal. The measured microarrays images represent a regular collection of spots, and the intensity of light at each spot is proportional to the DNA copy number or to the expression level of the gene whose DNA clone is spotted. Spot quality control is an essential part of microarray image analysis, which must be carried out at the level of individual spot identification. The problem is difficult to formalize due to the diversity of instrumental and biological factors that can influence the result.

Results
For each spot we estimate the ratio of measured fluorescence intensities revealing differential gene expression or change in DNA copy numbers between the test and control samples. We also define a set of quality characteristics and a model for combining these characteristics into an overall spot quality value. We have developed a training procedure to evaluate the contribution of each individual characteristic in the overall quality. This procedure uses information available from replicated spots, located in the same array or over a set of replicated arrays. It is assumed that unspoiled replicated spots must have very close ratios, whereas poor spots yield greater diversity in the obtained ratio estimates.

Conclusion
The developed procedure provides an automatic tool to quantify spot quality and to identify different types of spot deficiency occurring in DNA microarray technology. Quality values assigned to each spot can be used either to eliminate spots or to weight contribution of each ratio estimate in follow-up analysis procedures.
Microarray analysis of androgen-regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model
Authors: Petrusz Peter , Jeyaraj Durairaj A , Grossman Gail 
Published: December 2005

AbstractBackgroundSpermatogenesis is an androgen-dependent process, yet the molecular mechanisms of androgens' actions in testis are poorly understood. Transgenic mice overexpressing rat androgen-binding protein (ABP) in their testes have reduced levels of intratesticular androgens and, as a result, show a progressive impairment of spermatogenesis. We used this model to characterize changes in global gene expression in testis in response to reduced bioavailability of androgens.MethodsTotal RNA was extracted from testes of 30-day old transgenic and wild-type control mice, converted to cRNA, labeled with biotin, and hybridized to oligonucleotide microarrays. Microarray results were confirmed by real-time reverse transcription polymerase chain reaction.ResultsThree-hundred-eighty-one genes (3.05% of all transcripts represented on the chips) were up-regulated and 198 genes (1.59%) were down-regulated by at least a factor of 2 in the androgen-deficient animals compared to controls. Genes encoding membrane proteins, intracellular signaling molecules, enzymes, proteins participating in the immune response, and those involved in cytoskeleton organization were significantly overrepresented in the up-regulated group. Among the down-regulated transcripts, those coding for extracellular proteins were overrepresented most dramatically, followed by those related to proteolysis, cell adhesion, immune response, and growth factor, cytokine, and ion channel activities. Transcripts with the greatest potential impact on cellular activities included several transcription factors, intracellular signal transducers, secreted signaling molecules and enzymes, and various cell surface molecules. Major nodes in the up-regulated network were IL-6, AGT, MYC, and A2M, those in the down-regulated network were IL-2, -4, and -10, MAPK8, SOCS1, and CREB1.ConclusionMicroarray analysis followed by gene ontology profiling and connectivity analysis identified several functional groups of genes and individual genes responding to sustained reduction of androgen levels in the mouse testis. These include genes whose products function as transcription factors, cell surface molecules including ion channels, extra- and intracellular signaling molecules, and secreted enzymes with the potential of regulating cell-to-cell attachment. The transcription factors CREB1 (down-regulated) and MYC (up-regulated) may mediate the most important initial phases of the testicular response to reduced levels of androgens. These results suggest specific avenues for further research that will lead to a better understanding of how androgens regulate spermatogenesis.
New role for nuclear hormone receptors and coactivators in regulation of BRCA1-mediated DNA repair in breast cancer cell lines
Authors: Crowe David L , Lee Matt K 
Published: December 2005

Abstract
Introduction
The breast cancer susceptibility gene BRCA1 is involved in the repair of double-strand breaks induced by ionizing radiation and chemotherapy drugs. BRCA1 interacts with coactivators such as p300 and CREB-binding protein (CBP) to activate target gene transcription. Estrogen and retinoic acid receptors (ER and RAR) also require coactivator proteins for their ligand-dependent functions. Few studies have suggested a role for nuclear hormone receptors in DNA repair.

Methods
DNA damage and repair activity were quantified with the use of single-cell gel electrophoresis and plasmid end-joining assays. Cell cycle progression and apoptosis were determined by bromodeoxyuridine and TdT-mediated dUTP nick end labelling assays. Stable transfection was accomplished with the lipofection procedure. Protein interaction and expression were determined by immunoprecipitation and western blotting.

Results
17β-Estradiol (E2) and all-trans retinoic acid (RA) had opposing effects on DNA damage and breast cancer cell survival after double-strand break damage. Treatment with E2, but not with RA, resulted in complex formation between ERα, CBP, and BRCA1 in ER-positive cell lines. Mutant BRCA1 reduced the expression and activity of DNA damage repair proteins but did not block nuclear hormone-dependent effects. Mutant BRCA1 failed to form complexes with ERα and CBP, which correlated with its ability to exert E2-independent effects on DNA repair. Mutant BRCA1 inhibited cell cycle progression and produced increased survival in cells with double-strand breaks. Ectopic ERα expression reproduced the E2-mediated effects on DNA damage, repair, and survival.

Conclusion
The present study proposes a new mechanism by which ER and RAR regulate BRCA1-mediated DNA repair by means of CBP.
Overexpression of Kruppel-Like Factor 7 Regulates Adipocytokine Gene Expressions in Human Adipocytes and Inhibits Glucose-Induced Insulin Secretion in Pancreatic β-Cell Line
Authors: Kawamura Yoshihiro , Tanaka Yasushi , Kawamori Ryuzo , Maeda Shiro 
Published: December 2005

Abstract
We have identified Kruppel-like factor 7 (KLF7) as a new candidate for conferring susceptibility to type 2 diabetes. To ascertain the possible involvement of KLF7 in the pathogenesis of type 2 diabetes, we examined the functional roles of KLF7 in various types of cells. In human adipocytes overexpressing KLF7, the expression of adiponectin and leptin was decreased compared with that in control cells, whereas expression of IL-6 was increased. In the insulin-secreting cell line (HIT-T15 cells), the expression and glucose-induced secretion of insulin were significantly suppressed in KLF7-overexpressed cells compared with control cells, accompanied by the reduction in the expression of glucose transporter 2, sulfonylurea receptor 1, Kir6.2, and pancreatic-duodenal homeobox factor 1. We also found that the overexpression of KLF7 resulted in the decrease of hexokinase 2 expression in smooth muscle cells, and of glucose transporter 2 expression in the HepG2 cells. These results suggest that KLF7 may contribute to the pathogenesis of type 2 diabetes through an impairment of insulin biosynthesis and secretion in pancreatic β-cells and a reduction of insulin sensitivity in peripheral tissues. Therefore, we suggest that KLF7 plays an important role in the pathogenesis of type 2 diabetes, and may be a useful target for new drugs to aid in the prevention and treatment of this disease.
Regulation of Macrophage Inflammatory Gene Expression by the Orphan Nuclear Receptor Nur77
Authors: Pei Liming , Castrillo Antonio , Tontonoz Peter 
Published: December 2005

AbstractMembers of the nuclear hormone receptor superfamily have emerged as important regulators of macrophage gene expression in inflammation and disease. Previous studies have shown that the lipid-activated receptors peroxisomal proliferator-activated receptor and liver X receptor inhibit nuclear factor-κB (NF-κB) signaling and inflammatory gene expression. We recently identified the NR4A subfamily of orphan nuclear receptors (Nur77/NR4A1, Nurr1/NR4A2, and NOR1/NR4A3) as lipopolysaccharide- and NF-κB-responsive genes in macrophages. However, the role of these transcription factors in macrophage gene expression is unknown. We demonstrate here that, in contrast to peroxisomal proliferator-activated receptor and liver X receptor, the role of NR4A receptors in macrophages is proinflammatory. Retroviral expression of Nur77 in macrophages leads to the transcriptional activation of multiple genes involved in inflammation, apoptosis, and cell cycle control. One particularly interesting Nur77-responsive gene is the inducible kinase IKKi/IKKε, an important component of the NF-κB signaling pathway. The IKKi promoter contains a functional NR4A binding site and is activated by all three NR4A receptors in transient transfection assays. Consistent with the activation of IKKi, expression of Nur77 in macrophages potentiates the induction of inflammatory gene expression in response to lipopolysaccharide. These results identify a new role for NR4A orphan nuclear receptors in the control of macrophage gene expression during inflammation.
Repulsive Separation of the Cytoplasmic Ends of Transmembrane Helices 3 and 6 Is Linked to Receptor Activation in a Novel Thyrotropin Receptor Mutant (M626I)
Authors: Ringkananont Usanee , Van Durme Joost , Montanelli Lucia , Ugrasbul Figen , Yu Y. Miles , Weiss Roy E. , Refetoff Samuel , Grasberger Helmut 
Published: December 2005

AbstractLigand-dependent activation of G protein-coupled receptors (GPCRs) involves repositioning of the juxtacytoplasmic ends of transmembrane helices TM3 and TM6. This concept, inferred from site-directed spin labeling studies, is supported by chemical cross-linking of the cytoplasmic ends of TM3 and TM6 blocking GPCR activation. Here we report a novel constitutive active mutation (M626I) in TM6 of the TSH receptor (TSHR), identified in affected members of a family with nonautoimmune hyperthyroidism. The specific constitutive activity of M626I, measured by its basal cAMP generation corrected for cell surface expression, was 13-fold higher than that of wild-type TSHR. Homology modeling of the TSHR serpentine domain based on the rhodopsin crystal structure suggests that M626 faces the side chain of I515 of TM3 near the membrane-cytoplasmic junction. Steric hindrance of the introduced isoleucine by I515 is consistent with the fact that shorter or more flexible side chains at position 626 did not increase constitutivity. Furthermore, a reciprocal mutation at position 515 (I515M), when introduced into the M626I background, acts as revertant mutation by allowing accommodation of the isoleucine sidechain at position 626 and fully restoring the constitutive activity to the level of wild-type TSHR. Thus, repulsive separation of the juxtacytoplasmic TM6 and TM3 in the M626I model conclusively demonstrates a direct link between the opening of this cytoplasmic face of the receptor structure and G protein coupling.
Sequence-Specific Deoxyribonucleic Acid (DNA) Recognition by Steroidogenic Factor 1: A Helix at the Carboxy Terminus of the DNA Binding Domain Is Necessary for Complex Stability
Authors: Little Tanya H. , Zhang Yongbo , Matulis Christina K. , Weck Jennifer , Zhang Zhipeng , Ramachandran Aparna , Mayo Kelly E. , Radhakrishnan Ishwar 
Published: December 2005

AbstractSteroidogenic factor 1 (SF1) is a member of the NR5A subfamily of nuclear hormone receptors and is considered a master regulator of reproduction because it regulates a number of genes encoding reproductive hormones and enzymes involved in steroid hormone biosynthesis. Like other NR5A members, SF1 harbors a highly conserved approximately 30-residue segment called the FTZ-F1 box C-terminal to the core DNA binding domain (DBD) common to all nuclear receptors and binds to 9-bp DNA sequences as a monomer. Here we describe the solution structure of the SF1 DBD in complex with an atypical sequence in the proximal promoter region of the inhibin-α gene that encodes a subunit of a reproductive hormone. SF1 forms a specific complex with the DNA through a bipartite motif binding to the major and minor grooves through the core DBD and the N-terminal segment of the FTZ-F1 box, respectively, in a manner previously described for two other monomeric receptors, nerve growth factor-induced-B and estrogen-related receptor 2. However, unlike these receptors, SF1 harbors a helix in the C-terminal segment of the FTZ-F1 box that interacts with both the core DBD and DNA and serves as an important determinant of stability of the complex. We propose that the FTZ-F1 helix along with the core DBD serves as a platform for interactions with coactivators and other DNA-bound factors in the vicinity.
Comparative overwintering physiology of Alaska and Indiana populations of the beetle Cucujus clavipes (Fabricius): roles of antifreeze proteins, polyols, dehydration and diapause
Authors: Bennett Valerie A. , Sformo Todd , Walters Kent , Toien Oivind , Jeannet Kennan , Hochstrasser Ronald , Pan Qingfeng , Serianni Anthony S. , Barnes Brian M. , Duman John G. 
Published: December 2005

SUMMARY
The beetle Cucujus clavipes is found in North America over a broad latitudinal range from North Carolina (latitude ∼35°N) to near tree line in the Brooks Range in Alaska (latitude, ∼67°30′ N). The cold adaptations of populations from northern Indiana (∼41°45′N) and Alaska were compared and, as expected, the supercooling points (the temperatures at which they froze) of these freeze-avoiding insects were significantly lower in Alaska insects. Both populations produce glycerol, but the concentrations in Alaska larvae were much higher than in Indiana insects(∼2.2 and 0.5 mol l–1, respectively). In addition, both populations produce antifreeze proteins. Interestingly, in the autumn both populations have the same approximate level of hemolymph thermal hysteresis,indicative of antifreeze protein activity, suggesting that they synthesize similar amounts of antifreeze protein. A major difference is that the Alaska larvae undergo extreme dehydration in winter wherein water content decreases from 63–65% body water (1.70–1.85 g H2O g–1 dry mass) in summer to 28–40% body water(0.40–0.68 g H2O g–1 dry mass) in winter. These 2.5–4.6-fold reductions in body water greatly increase the concentrations of antifreeze in the Alaska insects. Glycerol concentrations would increase to 7–10 mol l–1 while thermal hysteresis increased to nearly 13°C (the highest ever measured in any organism) in concentrated hemolymph. By contrast, Indiana larvae do not desiccate in winter. The Alaska population also undergoes a diapause while insects from Indiana do not. The result of these, and likely additional, adaptations is that while the mean winter supercooling points of Indiana larvae were approximately –23°C, those of Alaska larvae were –35 to–42°C, and at certain times Alaska C. clavipes did not freeze when cooled to –80°C.