bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knockdown of c-Myc expression by RNAi inhibits MCF-7 breast tumor cells growth in vitro and in vivo
Authors: Wang Yi-hua , Liu Shuang , Zhang Guo , Zhou Cui-qi , Zhu Hong-xia , Zhou Xiao-bo , Quan Lan-ping , Bai Jin-feng , Xu Ning-zhi 
Published: January 2005

Abstract
Introduction
Breast cancer is the leading cause of cancer death in women worldwide. Elevated expression of c-Myc is a frequent genetic abnormality seen in this malignancy. For a better understanding of its role in maintaining the malignant phenotype, we used RNA interference (RNAi) directed against c-Myc in our study. RNAi provides a new, reliable method to investigate gene function and has the potential for gene therapy. The aim of the study was to examine the anti-tumor effects elicited by a decrease in the protein level of c-Myc by RNAi and its possible mechanism of effects in MCF-7 cells.

Method
A plasmid-based polymerase III promoter system was used to deliver and express short interfering RNA (siRNA) targeting c-myc to reduce its expression in MCF-7 cells. Western blot analysis was used to measure the protein level of c-Myc. We assessed the effects of c-Myc silencing on tumor growth by a growth curve, by soft agar assay and by nude mice experiments in vivo. Standard fluorescence-activated cell sorter analysis and TdT-mediated dUTP nick end labelling assay were used to determine apoptosis of the cells.

Results
Our data showed that plasmids expressing siRNA against c-myc markedly and durably reduced its expression in MCF-7 cells by up to 80%, decreased the growth rate of MCF-7 cells, inhibited colony formation in soft agar and significantly reduced tumor growth in nude mice. We also found that depletion of c-Myc in this manner promoted apoptosis of MCF-7 cells upon serum withdrawal.

Conclusion
c-Myc has a pivotal function in the development of breast cancer. Our data show that decreasing the c-Myc protein level in MCF-7 cells by RNAi could significantly inhibit tumor growth both in vitro and in vivo, and imply the therapeutic potential of RNAi on the treatment of breast cancer by targeting overexpression oncogenes such as c-myc, and c-myc might be a potential therapeutic target for human breast cancer.
High expression of focal adhesion kinase (p125FAK) in node-negative breast cancer is related to overexpression of HER-2/neu and activated Akt kinase but does not predict outcome
Authors: Schmitz Klaus Jürgen , Grabellus Florian , Callies Rainer , Otterbach Friedrich , Wohlschlaeger Jeremias , Levkau Bodo , Kimmig Rainer , Schmid Kurt Werner , Baba Hideo Andreas 
Published: January 2005

Abstract
Introduction
Focal adhesion kinase (FAK) regulates multiple cellular processes including growth, differentiation, adhesion, motility and apoptosis. In breast carcinoma, FAK overexpression has been linked to cancer progression but the prognostic relevance remains unknown. In particular, with regard to lymph node-negative breast cancer it is important to identify high-risk patients who would benefit from further adjuvant therapy.

Methods
We analyzed 162 node-negative breast cancer cases to determine the prognostic relevance of FAK expression, and we investigated the relationship of FAK with major associated signaling pathways (HER2, Src, Akt and extracellular regulated kinases) by immunohistochemistry and western blot analysis.

Results
Elevated FAK expression did not predict patient outcome, in contrast to tumor grading (P = 0.005), Akt activation (P = 0.0383) and estrogen receptor status (P = 0.0033). Significant positive correlations were observed between elevated FAK expression and HER2 overexpression (P = 0.001), as well as phospho-Src Tyr-215 (P = 0.021) and phospho-Akt (P < 0.001), but not with phospho-ERK1/2 (P = 0.108). Western blot analysis showed a significant correlation of FAK Tyr-861 activation and HER2 overexpression (P = 0.01).

Conclusions
Immunohistochemical detection of FAK expression is of no prognostic significance in node-negative breast cancer but provides evidence that HER2 is involved in tumor malignancy and metastatic ability of breast cancer through a novel signaling pathway participating FAK and Src.
Relative microvessel area of the primary tumour, and not lymph node status, predicts the presence of bone marrow micrometastases detected by reverse transcriptase polymerase chain reaction in patients with clinically non-metastatic breast cancer
Authors: Benoy Ina H , Salgado Roberto , Elst Hilde , Van Dam Peter , Weyler Joost , Van Marck Eric , Scharpé Simon , Vermeulen Peter B , Dirix Luc Y 
Published: January 2005

AbstractAbout 50% of patients with breast cancer have no involvement of axillary lymph nodes at diagnosis and can be considered cured after primary locoregional treatment. However, about 20–30% will experience distant relapse. The group of patients at risk is not well characterised: recurrence is probably due to the establishment of micrometastases before treatment. Given the early steps of metastasis in which tumour cells interact with endothelial cells of blood vessels, and, given the independent prognostic value in breast cancer of both the quantification of tumour vascularisation and the detection of micrometastases in the bone marrow, the aim of this study was to determine the relationship between vascularisation, measured by Chalkley morphometry, and the bone marrow content of cytokeratin-19 (CK-19) mRNA, quantified by real-time reverse transcriptase polymerase chain reaction, in a series of 68 patients with localised untreated breast cancer. The blood concentration of factors involved in angiogenesis (interleukin-6 and vascular endothelial growth factor) and of factors involved in coagulation (D-dimer, fibrinogen, platelets) was also measured. When bone marrow CK-19 relative gene expression (RGE) was categorised according to the cut-off value of 0.77 (95th centile of control patients), 53% of the patients had an elevated CK-19 RGE. Patients with bone marrow micrometastases, on the basis of an elevated CK-19 RGE, had a mean Chalkley count of 7.5 ± 1.7 (median 7, standard error [SE] 0.30) compared with a mean Chalkley count of 6.5 ± 1.7 in other patients (median 6, SE 0.3) (Mann–Whitney U-test; P = 0.04). Multiple regression analysis revealed that Chalkley count, not lymph node status, independently predicted CK-19 RGE status (P = 0.04; odds ratio 1.38; 95% confidence interval 1.009–1.882). Blood parameters reflecting angiogenesis and coagulation were positively correlated with Chalkley count and/or CK-19 RGE. Our data are in support of an association between elevated relative microvessel area of the primary tumour and the presence of bone marrow micrometastases in breast cancer patients with operable disease, and corroborate the paracrine and endocrine role of interleukin-6 and the involvement of coagulation in breast cancer growth and metastasis.
Common ERBB2 polymorphisms and risk of breast cancer in a white British population: a case–control study
Authors: Benusiglio Patrick R , Lesueur Fabienne , Luccarini Craig , Conroy Donald M , Shah Mitul , Easton Douglas F , Day Nick E , Dunning Alison M , Pharoah Paul D , Ponder Bruce AJ 
Published: January 2005

Abstract
Introduction
About two-thirds of the excess familial risk associated with breast cancer is still unaccounted for and may be explained by multiple weakly predisposing alleles. A gene thought to be involved in low-level predisposition to the disease is ERBB2 (HER2). This gene is involved in cell division, differentiation, and apoptosis and is frequently amplified in breast tumours. Its amplification correlates with poor prognosis. Moreover, the coding polymorphism I655V has previously been associated with an increased risk of breast cancer.

Methods
We aimed to determine if common polymorphisms (frequency ≥ 5%) in ERBB2 were associated with breast cancer risk in a white British population. Five single-nucleotide polymorphisms (SNPs) were selected for study: SNP 1 near the promoter, SNP 2 in intron 1, SNP 3 in intron 4, SNP 4 in exon 17 (I655V), and SNP 5 in exon 27 (A1170P). We tested their association with breast cancer in a large case–control study (n = 2192 cases and 2257 controls).

Results
There were no differences in genotype frequencies between cases and controls for any of the SNPs examined. To investigate the possibility that a common polymorphism not included in our study might be involved in breast cancer predisposition, we also constructed multilocus haplotypes. Our set of SNPs generated all existing (n = 6) common haplotypes and no differences were seen in haplotype frequencies between cases and controls (P = 0.44).

Conclusions
In our population, common ERBB2 polymorphisms are not involved in predisposition to breast cancer.
Extravascular lung water in patients with severe sepsis: a prospective cohort study
Authors: Martin Greg S , Eaton Stephanie , Mealer Meredith , Moss Marc 
Published: January 2005

Abstract
Introduction
Few investigations have prospectively examined extravascular lung water (EVLW) in patients with severe sepsis. We sought to determine whether EVLW may contribute to lung injury in these patients by quantifying the relationship of EVLW to parameters of lung injury, to determine the effects of chronic alcohol abuse on EVLW, and to determine whether EVLW may be a useful tool in the diagnosis of acute respiratory distress syndrome (ARDS).

Methods
The present prospective cohort study was conducted in consecutive patients with severe sepsis from a medical intensive care unit in an urban university teaching hospital. In each patient, transpulmonary thermodilution was used to measure cardiovascular hemodynamics and EVLW for 7 days via an arterial catheter placed within 72 hours of meeting criteria for severe sepsis.

Results
A total of 29 patients were studied. Twenty-five of the 29 patients (86%) were mechanically ventilated, 15 of the 29 patients (52%) developed ARDS, and overall 28-day mortality was 41%. Eight out of 14 patients (57%) with non-ARDS severe sepsis had high EVLW with significantly greater hypoxemia than did those patient with low EVLW (mean arterial oxygen tension/fractional inspired oxygen ratio 230.7 ± 36.1 mmHg versus 341.2 ± 92.8 mmHg; P < 0.001). Four out of 15 patients with severe sepsis with ARDS maintained a low EVLW and had better 28-day survival than did ARDS patients with high EVLW (100% versus 36%; P = 0.03). ARDS patients with a history of chronic alcohol abuse had greater EVLW than did nonalcoholic patients (19.9 ml/kg versus 8.7 ml/kg; P < 0.0001). The arterial oxygen tension/fractional inspired oxygen ratio, lung injury score, and chest radiograph scores correlated with EVLW (r2 = 0.27, r2 = 0.18, and r2 = 0.28, respectively; all P < 0.0001).

Conclusions
More than half of the patients with severe sepsis but without ARDS had increased EVLW, possibly representing subclinical lung injury. Chronic alcohol abuse was associated with increased EVLW, whereas lower EVLW was associated with survival. EVLW correlated moderately with the severity of lung injury but did not account for all respiratory derangements. EVLW may improve both risk stratification and management of patients with severe sepsis.
Computational prediction of human metabolic pathways from the complete human genome
Authors: Romero Pedro , Wagg Jonathan , Green Michelle L , Kaiser Dale , Krummenacker Markus , Karp Peter D 
Published: January 2005

Abstract
Background
We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary first step toward quantitative modeling of metabolism.

Results
Our analysis assigns 2,709 human enzymes to 896 bioreactions; 622 of the enzymes are assigned roles in 135 predicted metabolic pathways. The predicted pathways closely match the known nutritional requirements of humans. This analysis identifies probable omissions in the human genome annotation in the form of 203 pathway holes (missing enzymes within the predicted pathways). We have identified putative genes to fill 25 of these holes. The predicted human metabolic map is described by a Pathway/Genome Database called HumanCyc, which is available at http://HumanCyc.org/. We describe the generation of HumanCyc, and present an analysis of the human metabolic map. For example, we compare the predicted human metabolic pathway complement to the pathways of Escherichia coli and Arabidopsis thaliana and identify 35 pathways that are shared among all three organisms.

Conclusions
Our analysis elucidates a significant portion of the human metabolic map, and also indicates probable unidentified genes in the genome. HumanCyc provides a genome-based view of human nutrition that associates the essential dietary requirements of humans with a set of metabolic pathways whose existence is supported by the human genome. The database places many human genes in a pathway context, thereby facilitating analysis of gene expression, proteomics, and metabolomics datasets through a publicly available online tool called the Omics Viewer.
Genome-scale approaches for discovering novel nonconventional splicing substrates of the Ire1 nuclease
Authors: Niwa Maho , Patil Christopher K , DeRisi Joe , Walter Peter 
Published: January 2005

Abstract
Background
The unfolded protein response (UPR) allows intracellular feedback regulation that adjusts the protein-folding capacity of the endoplasmic reticulum (ER) according to need. The signal from the ER lumen is transmitted by the ER-transmembrane kinase Ire1, which upon activation displays a site-specific endoribonuclease activity. Endonucleolytic cleavage of the intron from the HAC1 mRNA (encoding a UPR-specific transcription factor) is the first step in a nonconventional mRNA splicing pathway; the released exons are then joined by tRNA ligase. Because only the spliced mRNA is translated, splicing is the key regulatory step of the UPR.

Results
We developed methods to search for additional mRNA substrates of Ire1p in three independent lines of genome-wide analysis. These methods exploited the well characterized enzymology and genetics of the UPR and the yeast genome sequence in conjunction with microarray-based detection. Each method successfully identified HAC1 mRNA as a substrate according to three criteria: HAC1 mRNA is selectively cleaved in vitro by Ire1; the HAC1 mRNA sequence contains two predicted Ire1 cleavage sites; and HAC1 mRNA is selectively degraded in tRNA ligase mutant cells.

Conclusion
Within the limits of detection, no other mRNA satisfies any of these criteria, suggesting that a unique nonconventional mRNA-processing mechanism has evolved solely for carrying out signal transduction between the ER and the nucleus. The approach described here, which combines biochemical and genetic 'fractionation' of mRNA with a novel application of cDNA microarrays, is generally applicable to the study of pathways in which RNA metabolism and alternative splicing have a regulatory role.
Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels
Authors: Tasneem Asba , Iyer Lakshminarayan M , Jakobsson Eric , Aravind L 
Published: January 2005

Abstract
Background
Acetylcholine receptor type ligand-gated ion channels (ART-LGIC; also known as Cys-loop receptors) are a superfamily of proteins that include the receptors for major neurotransmitters such as acetylcholine, serotonin, glycine, GABA, glutamate and histamine, and for Zn2+ ions. They play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the Metazoa.

Results
Using sensitive sequence-profile searches we have identified homologs of ART-LGICs in several bacteria and a single archaeal genus, Methanosarcina. The homology between the animal receptors and the prokaryotic homologs spans the entire length of the former, including both the ligand-binding and channel-forming transmembrane domains. A sequence-structure analysis using the structure of Lymnaea stagnalis acetylcholine-binding protein and the newly detected prokaryotic versions indicates the presence of at least one aromatic residue in the ligand-binding boxes of almost all representatives of the superfamily. Investigation of the domain architectures of the bacterial forms shows that they may often show fusions with other small-molecule-binding domains, such as the periplasmic binding protein superfamily I (PBP-I), Cache and MCP-N domains. Some of the bacterial forms also occur in predicted operons with the genes of the PBP-II superfamily and the Cache domains. Analysis of phyletic patterns suggests that the ART-LGICs are currently absent in all other eukaryotic lineages except animals. Moreover, phylogenetic analysis and conserved sequence motifs also suggest that a subset of the bacterial forms is closer to the metazoan forms.

Conclusions
From the information from the bacterial forms we infer that cation-pi or hydrophobic interactions with the ligand are likely to be a pervasive feature of the entire superfamily, even though the individual residues involved in the process may vary. The conservation pattern in the channel-forming transmembrane domains also suggests similar channel-gating mechanisms in the prokaryotic versions. From the distribution of charged residues in the prokaryotic M2 transmembrane segments, we expect that there will be examples of both cation and anion selectivity within the prokaryotic members. Contextual connections suggest that the prokaryotic forms may function as chemotactic receptors for low molecular weight solutes. The phyletic patterns and phylogenetic relationships suggest the possibility that the metazoan receptors emerged through an early lateral transfer from a prokaryotic source, before the divergence of extant metazoan lineages.
Using ontologies to describe mouse phenotypes
Authors: Gkoutos Georgios V , Green Eain CJ , Mallon Ann-Marie , Hancock John M , Davidson Duncan 
Published: January 2005

AbstractThe mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sources. This produces a framework with greater flexibility, power and economy than previous approaches. We discuss some of the issues this approach raises.
“Mechanics” of Molecular Assembly: Real-Time and In-Situ Analysis of Nano-to-Mesoscopic Scale Hierarchical Structures and Nonequilibrium Phenomena
Authors: Hashimoto Takeji 
Published: January 2005

Abstract
We have presented studies of the mechanics of molecular assembly for multicomponent molecular systems in the context of nonlinear and nonequilibrium phenomena. The studies cover the following three themes: (i) elucidation of space-time self-assembly of hierarchical structures, in the length scale ranging from nm to μm, of binary molecular mixtures via phase transition by means of real-time and in-situ analyses with various scattering methods and microscopy methods; (ii) elucidation of self-assembly of molecular mixtures under shear flow in the context of open nonequilibrium phenomena by means of newly developed rheo-optical methods, leading us to discover new dissipative structures as well as shear-induced phase transitions both from single-phase to two-phase and from two-phase to single-phase; (iii) elucidation of the influences of chemical bonds between different component polymers in block copolymers on microphase transition and ordered microdomain structures with nano-scale periodicity and various space-group symmetries and exploration of nano-fabrication methods of microdomain structures as templates in the context of nano-science and nano-technology of block copolymers. In each of the three themes, we highlight and emphasize the fact that polymer systems provide very good model systems for basic studies of nonlinear and nonequilibrium phenomena because of the fact that large structures evolve very slowly in polymer systems. The studies may give perspectives for creating advanced soft materials responsive to environmental stimuli and for understanding activities, adaptation, and evolution of living organisms.
Synthesis and Characterization of New Metal–Metal Bonded Heptabromo Porphyrin
Authors: Takagi Shigeru , Furuta Hiroyuki , Yagi Toshitaka , Yamada Hiroyuki 
Published: January 2005

Abstract
A new metal–metal bonded porphyrin [(hbtbpp)In–Mn(CO)5], where hbtbpp is the dianion of 2,3,7,8,12,13,17-heptabromo-5,10,15,20-tetrakis(3,5-di-t-butylphenyl)porphyrin, has been synthesized. In our attempt to synthesize the indium complex of octabromo porphyrin using the DMF method, we found that Br atom loss occurred in the process of metal insertion. When having synthesized the metal–metal bonded porphyrin by using a mixture of (heptabromoporphyrinato)indium and (octabromoporphyrinato)indium as the starting material, only heptabromo M–M bonded porphyrin was obtained. A large ring deformation of octabromo porphyrin disturbed the formation of the M–M bond. This heptabromo M–M porphyrin has shown high stability against electroreduction or photo-irradiation.
Synthesis, Characterization, and Thermal Stability of New Mononuclear Hydrogenperoxocopper(II) Complexes with N3O-Type Tripodal Ligands Bearing Hydrogen-Bonding Interaction Sites
Authors: Yamaguchi Syuhei , Kumagai Akinori , Nagatomo Shigenori , Kitagawa Teizo , Funahashi Yasuhiro , Ozawa Tomohiro , Jitsukawa Koichiro , Masuda Hideki 
Published: January 2005

Abstract
In order to understand the effect of an oxygen-containing ligand on the physico-chemical properties and reactivities of hydrogenperoxocopper complexes, new copper(II) complexes with the N3O-type tripodal ligand bearing pivalamido groups, N,N-bis(6-pivalamido-2-pyridylmethyl)glycine (Hbpga), and N,N-bis(6-pivalamido-2-pyridylmethyl)-β-alanine (Hbpaa), have been designed and synthesized. Copper(II) complexes without any external ligand and those with a monodentate ligand, such as azido and chloro, have been prepared and characterized with the aid of electronic absorption and ESR spectroscopic, cyclic voltammetric, and X-ray structure analytical methods. The redox potential values of the Cu(II) complexes, when they were compared with the Cu(II) complex of bis(6-pivalamido-2-pyridylmethyl)(2-pyridylmethyl)amine (bppa), reported previously, shifted toward the negative side upon the introduction of a carboxylate group in the place of one pyridine of bppa. Reactions of [Cu(bpga)]ClO4 (1a) and [Cu(bpaa)]PF6 (2a) with hydrogen peroxide in the presence of triethylamine in both MeCN and MeOH solutions gave mononuclear copper(II) complexes with hydrogenperoxide(1−), Cu–bpga–OOH (1d) and Cu–bpaa–OOH (2d) systems, respectively. The intense absorption bands, assignable to LMCT (HOO− → Cu(II)) and d–d bands, and ESR and resonance Raman spectra have revealed that they form trigonal bipyramidal copper complexes with OOH− in an end-on fashion. The thermal stabilities of 1d and 2d have also been studied by following the reduction rate of the LMCT bands at 283 K. Those of copper(II) complexes with hydrogenperoxide(1−) have been reduced in the order 1d &gt; 2d &gt;&gt; [Cu(bppa)(OOH)]+ (3d), all of which are rather stable compared with that of Cu(II)–tpa–OOH (tpa = tris(2-pyridylmethyl)amine). These findings indicate that the hydrogenperoxocopper(II) complexes are activated by introducing carboxylate coordination, although they are stabilized by hydrogen-bonding interactions.