bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
Authors: Liu Xiangdong , Jessen Walter J , Sivaganesan Siva , Aronow Bruce J , Medvedovic Mario 
Published: August 2007

Abstract

Background
Transcriptional modules (TM) consist of groups of co-regulated genes and transcription factors (TF) regulating their expression. Two high-throughput (HT) experimental technologies, gene expression microarrays and Chromatin Immuno-Precipitation on Chip (ChIP-chip), are capable of producing data informative about expression regulatory mechanism on a genome scale. The optimal approach to joint modeling of data generated by these two complementary biological assays, with the goal of identifying and characterizing TMs, is an important open problem in computational biomedicine.

Results
We developed and validated a novel probabilistic model and related computational procedure for identifying TMs by jointly modeling gene expression and ChIP-chip binding data. We demonstrate an improved functional coherence of the TMs produced by the new method when compared to either analyzing expression or ChIP-chip data separately or to alternative approaches for joint analysis. We also demonstrate the ability of the new algorithm to identify novel regulatory relationships not revealed by ChIP-chip data alone. The new computational procedure can be used in more or less the same way as one would use simple hierarchical clustering without performing any special transformation of data prior to the analysis. The R and C-source code for implementing our algorithm is incorporated within the R package gimmR which is freely available at http://eh3.uc.edu/gimm.

Conclusion
Our results indicate that, whenever available, ChIP-chip and expression data should be analyzed within the unified probabilistic modeling framework, which will likely result in improved clusters of co-regulated genes and improved ability to detect meaningful regulatory relationships. Given the good statistical properties and the ease of use, the new computational procedure offers a worthy new tool for reconstructing transcriptional regulatory networks.
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach
Authors: Andorf Carson , Dobbs Drena , Honavar Vasant 
Published: August 2007

Abstract

Background
Incorrectly annotated sequence data are becoming more commonplace as databases increasingly rely on automated techniques for annotation. Hence, there is an urgent need for computational methods for checking consistency of such annotations against independent sources of evidence and detecting potential annotation errors. We show how a machine learning approach designed to automatically predict a protein's Gene Ontology (GO) functional class can be employed to identify potential gene annotation errors.

Results
In a set of 211 previously annotated mouse protein kinases, we found that 201 of the GO annotations returned by AmiGO appear to be inconsistent with the UniProt functions assigned to their human counterparts. In contrast, 97% of the predicted annotations generated using a machine learning approach were consistent with the UniProt annotations of the human counterparts, as well as with available annotations for these mouse protein kinases in the Mouse Kinome database.

Conclusion
We conjecture that most of our predicted annotations are, therefore, correct and suggest that the machine learning approach developed here could be routinely used to detect potential errors in GO annotations generated by high-throughput gene annotation projects.
Editors Note : Authors from the original publication (Okazaki et al.: Nature 2002, 420:563–73) have provided their response to Andorf et al, directly following the correspondence.
miRAS: a data processing system for miRNA expression profiling study
Authors: Tian Feng , Zhang Huayue , Zhang Xinyu , Song Chi , Xia Yongjing , Wu Yiqing , Liu Xiangjun 
Published: August 2007

Abstract

Background
The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studies try to discover new miRNAs and reveal the miRNA expression profile in cancer using a SAGE-based total RNA clone method. However, the data processing of this method is labor-intensive with several different biological databases and more than ten data processing steps involved.

Results
With miRAS, miRNAs and possible miRNA candidates contained in the submitted sequencing data were obtained together with their expression profile. The functions of known and predicted miRNAs were then analyzed by miRNA target prediction followed by target gene annotations. Finally, to extract the biological significance of the miRNAs in the samples, further annotations of the known miRNA and target genes were performed by collecting the public expression datasets of miRNA and target genes in normal and cancer tissues.

Conclusion
We introduce a web-based analysis platform called miRNA Analysis System (miRAS), for processing and analyzing of the sequence data obtained from the total RNA clone method. The system was built on generalizing the study of a liver cancer cell line total RNA sequencing project. miRAS is freely available on the web.
Host-derived RANKL is responsible for osteolysis in a C4-2 human prostate cancer xenograft model of experimental bone metastases
Authors: Morrissey Colm , Kostenuik Paul L , Brown Lisha G , Vessella Robert L , Corey Eva 
Published: August 2007

Abstract

Background
C4-2 prostate cancer (CaP) cells grown in mouse tibiae cause a mixed osteoblastic/osteolytic response with increases in osteoclast numbers and bone resorption. Administration of osteoprotegerin (OPG) blocks these increases, indicating the critical role of RANKL in osteolysis in this model. The objective of our study was to investigate whether RANKL expressed by tumor cells (human origin) directly stimulates osteolysis associated with the growth of these cells in bone or whether the increased osteolysis is caused by RANKL expressed by the host environment cells (murine origin). The relative contribution of tumor-vs. host-derived RANKL has been difficult to establish, even with human xenografts, because murine and human RANKL are both capable of stimulating osteolysis in mice, and the RANKL inhibitors used to date (OPG and RANK-Fc) inhibit human and murine RANKL.

Methods
To address this question we used a neutralizing, antibody (huRANKL MAb), which specifically neutralizes the biological activities of human RANKL and thereby the contribution of C4-2 derived RANKL in this tibial injection model of experimental bone metastases.

Results
Administration of huRANKL MAb did not inhibit the osteolytic response of the bone to these cells, or affect the establishment and growth of the C4-2 tumors in this environment.

Conclusion
In conclusion, our results suggest that in this model, murine RANKL and not the tumor-derived human RANKL is the mediator of the osteolytic reaction associated with C4-2 growth in bone. We hypothesize that C4-2 cells express other factor/s inducing host production of RANKL, thereby driving tumor-associated osteolysis.
Factors associated with a measles outbreak in children admitted at Mahosot Hospital, Vientiane, Laos
Authors: Mayxay Mayfong , Khomthilat Tiengthong , Souvannasing Phoutthalavanh , Phounesavath Khamphouvanh , Vorasane Banlieng , Keomany Sommay , Douangdala Phouvieng , Philavong Khamseng , Srour Leila , Newton Paul N 
Published: August 2007

AbstractBackgroundIn 2002 and 2003 there were large outbreaks of measles in many provinces of Laos, including in Vientiane. We therefore conducted a study to determine risk factors associated with measles amongst children admitted at Mahosot Hospital, Vientiane.MethodsA retrospective case-control study was conducted in 50 children with clinical measles who were matched by age and sex with 50 healthy children (who had never had a febrile rash) living in the same villages as the cases.ResultsThe proportion of children with complete immunizations was significantly lower in the group with clinical measles compared to the controls [13/50 (26%) vs 34/50 (68%),P< 0.001). The percentage of children who had received measles vaccine at 9–23 months of age was significantly lower in the group with clinical measles compared to the healthy controls [12/50 (24%) vs 24/50 (48%),P= 0.01). The family educational and socio-economic status did not differ significantly (P> 0.05) between cases and controls.ConclusionThese results emphasize the importance of intensification of measles immunization coverage in Laos. The strengthening of campaigns with large, widespread high second dose coverage is likely to be a key measure to prevent further measles outbreaks in Laos (192 words).
An unexpected supraclavicular swelling
Authors: Patel Nishith NB , Shah Parin R , Wilson Eliie , Haray Puthcode N 
Published: August 2007

Abstract

Background
Colorectal cancer is the third commonest cause of cancer death in UK. It commonly metastasises to the liver but rarely to small bones.

Case presentation
We describe a case of a patient with adenocarcinoma of the descending colon who presented preoperatively with a right supraclavicular swelling. Subsequent imaging and cytology of the lesion revealed this to be a metastasis to the right clavicle resulting in a pathological fracture.

Conclusion
This report describes the rare occurrence of a colorectal metastasis to the clavicle. It emphasises that although bone metastases from primary colorectal tumours are rare events, they tend to metastasise to small, non-weight bearing bones. It also discusses the utility of isotope bone scanning and that on certain occasions this imaging method may prove to be equivocal. In such circumstances, biopsy or magnetic resonance imaging is more sensitive for the detection of bone metastases.
Facile: a command-line network compiler for systems biology
Authors: Siso-Nadal Fernando , Ollivier Julien F , Swain Peter S 
Published: August 2007

Abstract

Background
A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. It is therefore important to be able to easily investigate the effects of adding or removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics of a model for a range of parameter values.

Results
We present Facile, a Perl command-line tool for analysing the dynamics of a systems biology model. Facile implements the law of mass action to automatically compile a biochemical network (written as, for example, ) into scripts for analytical analysis (Mathematica and Maple), for simulation (XPP and Matlab), and for bifurcation analysis (AUTO). Facile automatically identifies mass conservations and generates the reduced form of a model with the minimum number of independent variables. This form is essential for bifurcation analysis, and Facile produces a C version of the reduced model for AUTO.

Conclusion
Facile is a simple, yet powerful, tool that greatly accelerates analysis of the dynamics of a biochemical network. By acting at the command-line and because of its intuitive, text-based input, Facile is quick to learn and can be incorporated into larger programs or into automated tasks.
Stabilin-2 is involved in lymphocyte adhesion to the hepatic sinusoidal endothelium via the interaction with αMβ2 integrin
Authors: Jung Mi-Yeon , Park Seung-Yoon , Kim In-San 
Published: August 2007

AbstractAlthough lymphocyte recirculation to the endothelium plays a critical role in the movement of immune cells from the blood into tissues and sites of inflammation, the mechanisms involved in lymphocyte trafficking via the hepatic circulation have yet to be elucidated fully. In this study, we investigated the role of stabilin-2, which is expressed specifically in the sinusoidal endothelium, in the adhesion of lymphocytes to the hepatic endothelium. Stabilin-2-expressing cells mediate the adhesion of PBLs. This interaction was attributed specifically to the interaction of stabilin-2 with αMβ2 integrin. Using mutant stabilin-2 molecules with deletions in the extracellular domain, we mapped the binding site for αMβ2 integrin to the fasciclin 1 (FAS1) domains of stabilin-2. The specificity of the interaction between αMβ2 integrin and the FAS1 domain was confirmed further by binding assays using neutralizing antibodies. More physiologically, we showed that the down-regulation of stabilin-2 results in the defective binding of lymphocytes to hepatic sinusoidal endothelial cells under conditions of static and physiological flow. Together, these data show that stabilin-2 can reconstitute the lymphocyte–endothelial adhesion cascade under physiological shear stress. We propose a critical role for stabilin-2 in lymphocyte adhesion to specialized endothelia, such as that of the hepatic sinusoid.
A phenotypic and functional characterization of NK cells in adenoids
Authors: Mizrahi Sa’ar , Yefenof Eitan , Gross Menahem , Attal Pierre , Ben Yaakov Avraham , Goldman-Wohl Debra , Maly Bella , Stern Noam , Katz Gil , Gazit Roi , Sionov Ronit Vogt , Mandelboim Ofer , Chaushu Stella 
Published: August 2007

AbstractAdenoids are part of the MALT. In the present study, we analyzed cell surface markers and cytolytic activity of adenoidal NK (A-NK) cells and compared them with NK cells derived from blood of the same donors (B-NK). NK cells comprised 0.67% (0.4–1.2%) of the total lymphoid population isolated from adenoids. The majority (median=92%) of the A-NK cells was CD56brightCD16–. A-NK cells were characterized by the increased expression of activation-induced receptors. NKp44 was detected on &gt;60%, CD25 on &gt;40%, and HLA-DR on &gt;50% of freshly isolated A-NK cells. Functional assays indicated that the cytotoxic machinery of A-NK is intact, and sensitive target cells are killed via natural cytotoxicity receptors, such as NKG2D. Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1; CD66) expression was up-regulated in 23% (median) of the A-NK cells by IL-2 activation but unchanged in B-NK cells. CEACAM1 inhibited the A-NK killing of target cells. CXCR4 was expressed on more than 40% A-NK cells prior to activation. Its ligand, CXCL12, was found in endothelial cells of the capillaries within the adenoid and in cells of the epithelial lining. In addition, A-NK cells migrated in vitro toward a gradient of CXCL12 in a dose-responsive manner, suggesting a role for this chemokine in A-NK cell recruitment and trafficking. We conclude that the A-NK cells are unique in that they display an activated-like phenotype and are different from their CD16– B-NK cell counterparts. This phenotype presumably reflects the chronic interaction of A-NK cells with antigens penetrating the body through the nasal route.
Neuroprotective activities of CD4+CD25+ regulatory T cells in an animal model of Parkinson’s disease
Authors: Reynolds Ashley D , Banerjee Rebecca , Liu Jianou , Gendelman Howard E , Lee Mosley R 
Published: August 2007

AbstractProgressive loss of dopaminergic neurons in the substantia nigra pars compacta and their terminal connections in the striatum are central features in Parkinson’s disease (PD). Emerging evidence supports the notion that microglia neuroinflammatory responses speed neurodegenerative events. We demonstrated previously that this can be slowed by adoptive transfer of T cells from Copolymer-1-immunized mice administered to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) recipients. The cellular basis for this neuroprotective response was the CD4+ T cell population, suggesting involvement of CD4+CD25+ regulatory T cells (Tregs), cells known to suppress immune activation and maintain immune homeostasis and tolerance. We show for the first time that adoptive transfer of CD3-activated Tregs to MPTP-intoxicated mice provides greater than 90% protection of the nigrostriatal system. The response was dose-dependent and paralleled modulation of microglial responses and up-regulation of glial cell-derived neurotrophic factor (CDNF) and TGF-β. Interestingly, that adoptive transfer of effector T cells showed no significant neuroprotective activities. Tregs were found to mediate neuroprotection through suppression of microglial responses to stimuli, including aggregated, nitrated α-synuclein. Moreover, Treg-mediated suppression was also operative following removal of Tregs from culture prior to stimulation. This neuroprotection was achieved through modulation of microglial oxidative stress and inflammation. As Tregs can be modulated in vivo, these data strongly support the use of such immunomodulatory strategies to treat PD.
Conformational activation of CD11b without shedding of L-selectin on circulating human neutrophils
Authors: Orr Y , Taylor J M , Cartland S , Bannon P G , Geczy C , Kritharides L 
Published: August 2007

AbstractMembrane-activated complex 1 (Mac-1; CD11b/CD18) is a β2 integrin implicated in the pathophysiology of neutrophil-mediated tissue injury whose functional capacity is determined by stimulus-induced conformational activation rather than up-regulation. Mac-1 up-regulation and conformational activation, together with shedding of L-selectin, are reported after in vitro neutrophil activation. However, their regulation on circulating human neutrophils during acute inflammation is unclear. Using flow cytometry, we investigated neutrophil expression of Mac-1, its activation-reporter neo-epitope CBRM1/5, and L-selectin during the inflammatory stimulus of cardiac surgery. A subpopulation of circulating neutrophils expressed CBRM1/5 (CBRM1/5+) under basal conditions (6.28±2.59%) and was persistently expanded (9.95±4.0%–15.2±4.2%; P&lt;0.0001) peri-operatively, whereas total CD11b expression increased only transiently, intra-operatively. L-selectin expression was unchanged on CBRM1/5+ neutrophils, and soluble L-selectin levels decreased intra-operatively (P&lt;0.01), indicating that L-selectin was not shed. Increased CBRM1/5 expression without L-selectin loss or CD11b up-regulation was replicated in vitro by neutrophil stimulation with IL-8, C3a, and platelet-activating factor. Heparin, a known CD11b ligand, which is administered during cardiac surgery, markedly reduced neutrophil expression of conformationally active CD11b in vivo and in vitro, identifying a potential mechanism for its anti-inflammatory properties. We conclude that conformational activation of CD11b occurs on circulating neutrophils in vivo and can occur in the absence of CD11b up-regulation and L-selectin shedding.
A 5.8-kDa component of manuka honey stimulates immune cells via TLR4
Authors: Tonks A J , Dudley E , Porter N G , Parton J , Brazier J , Smith E L , Tonks A 
Published: August 2007

AbstractHoney is used as a therapy to aid wound healing. Previous data indicate that honey can stimulate cytokine production from human monocytes. The present study further examines this phenomenon in manuka honey. As inflammatory cytokine production in innate immune cells is classically mediated by pattern recognition receptors in response to microorganisms, bacterial contamination of honey and the effect of blocking TLR2 and -4 on stimulatory activity were assessed. No vegetative bacteria were isolated from honey; however, bacterial spores were cultured from one-third of samples, and low levels of LPS were detected. Blocking TLR4 but not TLR2 inhibited honey-stimulated cytokine production significantly. Cytokine production did not correlate with LPS levels in honey and was not inhibited by polymyxin B. Further, the activity was reduced significantly following heat treatment, indicating that component(s) other than LPS are responsible for the stimulatory activity of manuka honey. To identify the component responsible for inducing cytokine production, honey was separated by molecular weight using microcon centrifugal filtration and fractions assessed for stimulatory activity. The active fraction was analyzed by MALDI-TOF mass spectroscopy, which demonstrated the presence of a number of components of varying molecular weights. Additional fractionation using miniaturized, reverse-phase solid-phase extraction resulted in the isolation of a 5.8-kDa component, which stimulated production of TNF-α via TLR4. These findings reveal mechanisms and components involved in honey stimulation of cytokine induction and could potentially lead to the development of novel therapeutics to improve wound healing for patients with acute and chronic wounds.
Improving prescription quality in an in-patient mental health unit: three cycles of clinical audit
Authors: Ved Priti , Coupe Tim 
Published: August 2007

Aims and MethodWe undertook three cycles of clinical audit of prescription charts to improve the quality of the prescriptions written in an in-patient unit. Pharmacy and medical staff reviewed a total of 1466 prescriptions on 242 prescription charts against local guidelines and provided feedback to medical staff. The pharmacist also regularly reviewed prescription charts on the wards between audits.ResultsAfter three cycles of audit, 99.5% of prescriptions written were legible. The recording of drug allergies, section 58 status and patient age remained poor.Clinical ImplicationsA combination of clinical audit and continual pharmacist review of prescription charts can improve the quality of prescriptions written by medical staff in an in-patient unit.
A Simple Route to Preparation and Characterization of Er2O3 Microspheres
Authors: Han Kaidong , Zhang Youjin , Fang Zhiyong , Cheng Tao , Gao Minrui 
Published: August 2007

Abstract
Large scale, uniform Er2O3 microspheres have been prepared with CO(NH2)2 as the precipitant through a hydrothermal method. The obtained products were characterized by X-ray powder diffraction, X-ray photoelectron spectroscopy, transmission electron microscopy, and field-emission scanning electron microscopy. The Er2O3 microspheres are composed of nanoparticles, and the diameter is in the range of 200–300 nm. In addition, a possible formation mechanism of Er2O3 microspheres was discussed.
Oxidative Degradation of Nylon-6 and Nylon-6,6 with Nitrogen Dioxide in Supercritical Carbon Dioxide
Authors: Yanagihara Naohisa , Abe Naoto , Takama Hironori , Shimamura Yuichiro , Yoshida Masaaki 
Published: August 2007

Abstract
Nylon-6 and nylon-6,6 were subjected to oxidative degradation with NO2 in supercritical CO2. It was found that valuable short-chain α,ω-diacid mixture could be obtained in good yield under relatively mild conditions.
Preparation of Gold Nanoparticles by the Laser Ablation in Room-temperature Ionic Liquids
Authors: Kimura Yoshifumi , Takata Hiroshi , Terazima Masahide , Ogawa Tetsuo , Isoda Seiji 
Published: August 2007

Abstract
Gold nanoparticles have been prepared by the laser ablation of a gold plate in imidazolium-based ionic liquids. The size and stability of gold nanoparticles were dependent on the wavelength of the laser light and the alkyl-chain length of the imidazolium-based cation.
Synthesis of Tetragonal ZrO2 Nanocrystals with a High Proton Conductivity
Authors: Wang Hui , Qiu Xiaoqing , Li Liping , Li Guangshe 
Published: August 2007

Abstract
Pure tetragonal ZrO2 nanocrystals were prepared at low temperature (85 °C). Their proton conductivity measured at 80 °C in N2 is 5.63×10−5 S/cm which is one order of magnitude higher than that of 1.72×10−6 S/cm for the sulfated counterpart or of 4.17×10−6 S/cm reported in the literature for 3-nm crystals of ZrO2·nH2O.