bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural analysis of the lipid A derived from the lipopolysaccharide of Brucella abortus
Authors: Qureshi N. , Takayama K. , Seydel U. , Wang R. , Cotter R.J. , Agrawal P.K. , Bush C.A. , Kurtz R. , Berman D.T. 
Published: January 2008

Lipopolysaccharide (LPS) of Brucella abortus strain 45/20 was purified using a novel method. Monophosphoryl lipid A (MPLA) was prepared from this LPS, methylated, and purified by high performance liquid chromatography. Chemical, mass spectral, and nuclear magnetic resonance analyses showed that MPLA consists of heptaacyl lipid As with molecular weights of 2095, 2123, 2151 and 2179. They contained the β-1,6-linked 2,3-diamino-2,3,-dideoxy-glucose disaccharide backbone and a phosphate group at the 4' position. Bisphosphoryl lipid A was also prepared and completely O-deacylated. It contained an additional phosphate group, and either 2 hydroxyhexadecanoic, 1 hydroxytetradecanoic, 1 hydroxydodecanoic acids or 2 hydroxyhexadecanoic and 2 hydroxydodecanoic acids, all in amide linkage. The predominant ester-linked fatty acyl group in acyloxyacyl linkage was hexadecanoate. The purified LPS, bisphosphoryl lipid A, and MPLA from B. abortus showed about 14%, 3% and 1%, respectively, of the B cell mitogen activity of ReLPS from Escherichia coli at 1.0 μg/ml.
Deactivation of the respiratory burst of human and murine macrophages by lipopolysaccharide is a receptor mediated effect independent from autocrine mechanisms
Authors: Schneemann M. , Schaffner A. 
Published: January 2008

Endotoxin blunts secretion of reactive oxygen intermediates by macrophages. Because transforming growth factor β (TGFβ) or interleukin 10 (IL-10) were shown to deactivate macrophages, and are secreted by macrophages in response to LPS, we sought for autocrine mechanisms of macrophage deactivation by endotoxin. TGFβ did not deactivate the respiratory burst of human blood-derived and resident or thioglycollate-induced murine peritoneal macrophages. According to previous reports, suppression of H202 secretion by TGFβ was restricted to periodate-elicited murine peritoneal macrophages. In contrast to TGFβ, IL-10 deactivated systems producing reactive oxygen intermediates in human blood-derived human macrophages, but neither anti-TGFβ1 nor anti-IL-10 antibodies restored LPS-mediated deactivation of macrophages. Supernatants from LPS-treated human blood-derived macrophages could not confer deactivation to homologous macrophages. Deactivation by LPS required the presence of serum proteins and appeared to be mediated by the CD14 antigen-related LPS receptor, because anti-CD14 antibody and IL-4, which downregulates CD14, antagonized the LPS effect. Taken together, these observations indicate that the suppressive effect of LPS on the respiratory burst of macrophages is lipid A receptor-dependent, and results in a direct deactivation response of the cell without mediation by autocrine mechanisms.
G-CSF - an anti-inflammatory cytokine
Authors: Hartung T. , Volk H-D. , Wendel A. 
Published: January 2008

We have previously reported that in various macrophage populations prepared from G-CSF treated rats LPS-inducible TNF release was suppressed. In vitro, LPS induced liver cell death only when hepatocytes were cocultured with liver macrophages. Rat Kupffer cells from G-CSF treated donor animals were less potent in mediating LPS-inducible hepatocytotoxicity in vitro than cells from control animals. These ex vivo findings were confirmed in vivo by demonstrating that G-CSF treatment attenuated LPS-inducible circulating TNF levels and protected from liver injury and mortality. We extended these observations to humans in two studies with G-CSF treated volunteers. In a pilot study, 11 subjects were treated single-blindly with 480 μg G-CSF s.c. (n = 7) or saline placebo (n = 4). Blood was taken at different time-points relative to G-CSF injection and cytokine release capacity was assessed in LPS stimulated whole blood incubations. In blood from G-CSF treated volunteers, we found reduced LPS-inducible TNF formation while the release of both soluble TNF receptor (sTNF-R) and interleukin 1 receptor antagonist (IL-1ra) were increased. In a second double-blind, randomized and controlled study, three groups of seven volunteers were treated once or twice 24 h apart with G-CSF or solvent placebo. Besides LPS, various stimuli were included to initiate cytokine release in a whole blood assay. The reduction of TNF formation (mean 53 % at 24 h after G-CSF) was different with the various stimuli. All stimuli increased IL-1ra (mean 14-fold) and sTNF-R (mean 3-fold) at 24 h after G-CSF. LPS-inducible IFN-γ and GM-CSF were significantly reduced. Our data indicate that the pattern of cytokines produced by human whole blood taken after G-CSF treatment in response to a variety of stimuli is shifted from pro- to anti-inflammatory mediators. These findings extend the knowledge on the pharmacology of G-CSF in animal models of the systemic inflammatory response syndrome and prompt a trial of G-CSF prophylaxis with this indication.
Ascorbic Acid Retention and Organoleptic Quality of Green Vegetables Cooked by Several Techniques Using Ammonium Bicarbonate1
Authors: Odland Dianne , Eheart Mary S. 
Published: January 2008

Five fresh green vegetables were cooked in small amounts of water (control), small amounts of water to which ammonium bicarbonate (NH4HCO3) had been added, and four of the five were also cooked in large amounts of water. Samples were analyzed for pH, titratable acidity, reduced and dehydro ascorbic acid, and color difference. The addition of NH4HCO3 to small amounts of water was found to be a more effective method of preserving color and ascorbic acid than the use of large amounts of water.Four commercially frozen green vegetables were cooked by package directions (control), in NH4HCO3 solution, and three of the four in ammonium bicarbonate ‐ calcium acetate (NH4HCO3 ‐ CaAc2) solution. The vegetables were analyzed for the same parameters described for fresh vegetables. Use of NH4HCO3 was again found to be an effective method for retention of color during cooking. The addition of CaAc2 prevented some of the adverse effects of the NH4HCO3 on firmness of the vegetables. Ascorbic acid losses were unaffected by either NH4HCO3 treatment.
Housing Decisions in Selecting a Residence in a Planned Townhouse Development
Authors: Gallogly Frances D. 
Published: January 2008

The process by which families decide to locate in a planned townhouse conarnurtity was studied in the context of a model of the decision‐making process involving “predictor,” “selection process,” and “outcomes of move” variables, using chi‐square analysis and contingency coefficients. The data were obtained through interviews using a structured questionnaire.The community studied was demographically fairly homogeneous. While housing space was of primary importance in decisions to move and housirtg specifications set while exploring the market, the physical appearance of the neighborhood and recreational facilities available proved important attractions to the community.Accessibility to place of employment was not of prime importance in housing decisions. The data supported prior theory that residential location really consists of two separate but linked decisions‐the decision to move and the decision to buy with an intervening search process. Some of the problems as well as the appeals of new planned communities were explored.
Hospitality Education and the Technological Revolution
Authors: Andrew William P. 
Published: January 2008

New advances in technology pervade nearly every aspect of our society, and hospitality is certainly no exception. Hospitality graduates entering the field find themselves surrounded by computerized point of sale, bar management, hotel reservation and front office, energy management, menu scoring, and accounting and inventory systems, along with such computer-controlled cooking equipment as friers and microvraves. Unfortunately, many of these hospitality graduates lack a basic understanding of how this technology will affect their professional roles or the overall direction of the industry. Thus, it is critical that hospitality education programs place more emphasis on providing their students with this understanding. To be able to do this efficiently and effectively, however, we need to understand the reasons why difficulties presently exist and how they may ultimately be resolved.
Quality Control Activities for Total Management in Japanese Hotels
Authors: Kaneto Noriharu 
Published: January 2008

Many people have been amazed by the present level of economic prosperity in Japan. What is not realized is the fact that Quality Control has been the most significant contributing factor to this rise. It has been proven advantageous to have a complete understanding of Quality Control activities. This paper explains in a step-by-step fashion the implementation of a QC program, the guidelinesfor the development of QC activities, the procedurefor introducing QC circles to Service Indiistries, and the advantages of utilizing this program in a hotel cotttpany. An actual QC seminar has been outlined and aids in developing a true understanding of the program.
Alcohol and The Liver
Authors: Sherlock Dame Sheila 
Published: January 2008

The association of alcohol with cirrhosis has been recognised for centuries. Worldwide, the consumption of alcohol is increasing. It is, however, becoming less in France (Government propaganda) and in the United States (changing life styles). Only 10-15% of those who abuse alcohol will develop cirrhosis. Risk factors are uncertain, but include dose and duration of alcohol consumption and female sex. Genetic differences in the metabolism of alcohol are important. Nutrition is of less importance. Alcohol is predominantly metabolised in the liver, the maximum is 160 to 180 g/day. 1 gm alcohol gives 7 calories and the alcoholic literally runs on spirit. The mechanisms by which the liver is damaged are uncertain. One factor may be acetaldehyde which is generated when alcohol is metabolised and is highly toxic. The changes in the liver go from fatty change, to acute alcoholic hepatitis, to cirrhosis and occasionally to liver cancer. Early recognition of alcoholic liver damage depends on the physician's suspicions, digestive symptoms, enlarged liver and an increase in the blood of liver enzymes (transaminases and especially, gammaglutamyl transpeptidase (Gamma GT). The red blood cells are increased in size (macrocytosis). Acute alcoholic hepatitis follows heavy consumption without eating. The patient is jaundiced and toxic and there is a high mortality. Cirrhosis is the end-stage of alcoholic liver damage. It is marked by jaundice, fluid in the belly (ascites), mental changes and bleeding from veins in the food pipe (oesophageal varices). Cirrhosis is irreversible. The outlook for cirrhosis in alcoholics is better than for other forms of cirrhosis, particularly if the patient abstains. The treatment otherwise is along the lines of any other form of chronic liver disease. Alcoholic cirrhosis is a self-inflicted disease. Donor organs are in short supply and there may be reluctance to consider liver transplantation. It is reserved for those with end-stage disease, who have been abstinent for at least 6 months, have a good job to return to, good family support and no other alcohol-related disease. The results are the same as for other types of cirrhosis. About 10% return to alcoholism after the transplant. ■
Down-regulation of Mpl marks the transition to lymphoid-primed multipotent progenitors with gradual loss of granulocyte-monocyte potential
Authors: Luc Sidinh , Anderson Kristina , Kharazi Shabnam , Buza-Vidas Natalija , Böiers Charlotta , Jensen Christina T. , Ma Zhi , Wittmann Lilian , Jacobsen Sten Eirik W. 
Published: January 2008

AbstractEvidence for a novel route of adult hematopoietic stem-cell lineage commitment through Lin−Sca-1+Kit+Flt3hi (LSKFlt3hi) lymphoid-primed multipotent progenitors (LMPPs) with granulocyte/monocyte (GM) and lymphoid but little or no megakaryocyte/erythroid (MkE) potential was recently challenged, as LSKFlt3hi cells were reported to possess MkE potential. Herein, residual (1%-2%) MkE potential segregated almost entirely with LSKFlt3hi cells expressing the thrombopoietin receptor (Mpl), whereas LSKFlt3hiMpl− LMPPs lacked significant MkE potential in vitro and in vivo, but sustained combined GM and lymphoid potentials, and coexpressed GM and lymphoid but not MkE transcriptional lineage programs. Gradually increased transcriptional lymphoid priming in single LMPPs from Rag1GFP mice was shown to occur in the presence of maintained GM lineage priming, but gradually reduced GM lineage potential. These functional and molecular findings reinforce the existence of GM/lymphoid-restricted progenitors with dramatically down-regulated probability for committing toward MkE fates, and support that lineage restriction occurs through gradual rather than abrupt changes in specific lineage potentials.
EAPB0203, a member of the imidazoquinoxaline family, inhibits growth and induces caspase-dependent apoptosis in T-cell lymphomas and HTLV-I–associated adult T-cell leukemia/lymphoma
Authors: Moarbess Georges , El-Hajj Hiba , Kfoury Youmna , El-Sabban Marwan E. , Lepelletier Yves , Hermine Olivier , Deleuze-Masquéfa Carine , Bonnet Pierre-Antoine , Bazarbachi Ali 
Published: January 2008

AbstractImiquimod is an immune response modifier currently used as a topical treatment of genital warts, basal cell carcinoma, cutaneous metastasis of malignant melanoma, and vascular tumors. We developed more efficient killers from the same family of compounds that can induce apoptosis without the prominent pro-inflammatory response associated with imiquimod. Among these new products, tk;4EAPB0203, a member of the imidazo[1,2-a]quinoxalines, exhibits an important cytotoxic activity in vitro. HTLV-I–associated adult T-cell leukemia (ATL) and HTLV-I–negative peripheral T-cell lymphomas are associated with poor prognosis. Using potentially achievable concentrations of EAPB0203, we demonstrate inhibition of cell proliferation, G2/M cell- cycle arrest, and induction of apoptosis in HTLV-I–transformed and HTLV-I–negative malignant T cells and fresh ATL cells, whereas normal resting or activated T lymphocytes were resistant. EAPB0203 treatment significantly down-regulated the antiapoptotic proteins c-IAP-1 and Bcl-XL and resulted in a significant loss of mitochondrial membrane potential, cytoplasmic release of cytochrome c, and caspase-dependent apoptosis. Moreover, in HTLV-I–transformed cells only, EAPB0203 treatment stabilized p21 and p53 proteins but had no effect on NF-κB activation. These results support a potential therapeutic role for EAPB0203 in ATL and HTLV-I–negative T-cell lymphomas, either as a systemic or topical therapy for skin lesions.
Structural and functional effects of hereditary hemolytic anemia-associated point mutations in the alpha spectrin tetramer site
Authors: Gaetani Massimiliano , Mootien Sara , Harper Sandra , Gallagher Patrick G. , Speicher David W. 
Published: January 2008

AbstractThe most common hereditary elliptocytosis (HE) and hereditary pyropoikilocytosis (HPP) mutations are α-spectrin missense mutations in the dimer-tetramer self-association site. In this study, we systematically compared structural and functional properties of the 14 known HE/HPP mutations located in the α-spectrin tetramer binding site. All mutant α-spectrin recombinant peptides were well folded, stable structures, with only the R34W mutant exhibiting a slight structural destabilization. In contrast, binding affinities measured by isothermal titration calorimetry were greatly variable, ranging from no detectable binding observed for I24S, R28C, R28H, R28S, and R45S to approximately wild-type binding for R34W and K48R. Binding affinities for the other 7 mutants were reduced by approximately 10- to 100-fold relative to wild-type binding. Some sites, such as R28, were hot spots that were very sensitive to even relatively conservative substitutions, whereas other sites were only moderately perturbed by nonconservative substitutions. The R34W and K48R mutations were particularly intriguing mutations that apparently either destabilize tetramers through mechanisms not probed by the univalent tetramer binding assay or represent polymorphisms rather than the pathogenic mutations responsible for observed clinical symptoms. All α0 HE/HPP mutations studied here appear to exert their destabilizing effects through molecular recognition rather than structural mechanisms.
Blocking binding of Bacillus thuringiensis Cry1Aa to Bombyx mori cadherin receptor results in only a minor reduction of toxicity
Authors: You Taek H , Lee Mi K , Jenkins Jeremy L , Alzate Oscar , Dean Donald H 
Published: January 2008

Abstract

Background

Bacillus thuringiensis Cry1Aa insecticidal protein is the most active known B. thuringiensis toxin against the forest insect pest Lymantria dispar (gypsy moth), unfortunately it is also highly toxic against the non-target insect Bombyx mori (silk worm).

Results
Surface exposed hydrophobic residues over domains II and III were targeted for site-directed mutagenesis. Substitution of a phenylalanine residue (F328) by alanine reduced binding to the Bombyx mori cadherin by 23-fold, reduced biological activity against B. mori by 4-fold, while retaining activity against Lymantria dispar.

Conclusion
The results identify a novel receptor-binding epitope and demonstrate that virtual elimination of binding to cadherin BR-175 does not completely remove toxicity in the case of B. mori.
miRNAminer: A tool for homologous microRNA gene search
Authors: Artzi Shay , Kiezun Adam , Shomron Noam 
Published: January 2008

Abstract

Background
MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experimental and computational methods were used to construct miRNA gene repositories agreeing with careful submission guidelines.

Results
An algorithm we developed – miRNAminer – is used for homologous conserved miRNA gene search in several animal species. Given a search query, candidate homologs from different species are tested for their known miRNA properties, such as secondary structure, energy and alignment and conservation, in order to asses their fidelity. When applying miRNAminer on seven mammalian species we identified several hundreds of high-confidence homologous miRNAs increasing the total collection of (miRbase) miRNAs, in these species, by more than 50%. miRNAminer uses stringent criteria and exhibits high sensitivity and specificity.

Conclusion
We present – miRNAminer – the first web-server for homologous miRNA gene search in animals. miRNAminer can be used to identify conserved homolog miRNA genes and can also be used prior to depositing miRNAs in public databases. miRNAminer is available at http://pag.csail.mit.edu/mirnaminer.
Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service
Authors: Kim Jeong-Gu , Park Daeui , Kim Byoung-Chul , Cho Seong-Woong , Kim Yeong Tae , Park Young-Jin , Cho Hee Jung , Park Hyunseok , Kim Ki-Bong , Yoon Kyong-Oh , Park Soo-Jun , Lee Byoung-Moo , Bhak Jong 
Published: January 2008

Abstract

Background
Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysaccharides production, toxins release, iron acquisition, and effector proteins secretion. Many such mechanisms involve some kind of protein-protein interaction in hosts. Our first aim was to predict the whole protein interaction pairs (interactome) of Xanthomonas oryzae pathovar oryzae (Xoo) that is an important pathogenic bacterium that causes bacterial blight (BB) in rice. We developed a detection protocol to find possibly interacting proteins in its host using whole genome PPI prediction algorithms. The second aim was to build a DB server and a bioinformatic procedure for finding target proteins in Xoo for developing pesticides that block host-pathogen protein interactions within critical biochemical pathways.

Description
A PPI network in Xoo proteome was predicted by bioinformatics algorithms: PSIMAP, PEIMAP, and iPfam. We present the resultant species specific interaction network and host-pathogen interaction, XooNET. It is a comprehensive predicted initial PPI data for Xoo. XooNET can be used by experimentalists to pick up protein targets for blocking pathological interactions. XooNET uses most of the major types of PPI algorithms. They are: 1) Protein Structural Interactome MAP (PSIMAP), a method using structural domain of SCOP, 2) Protein Experimental Interactome MAP (PEIMAP), a common method using public resources of experimental protein interaction information such as HPRD, BIND, DIP, MINT, IntAct, and BioGrid, and 3) Domain-domain interactions, a method using Pfam domains such as iPfam. Additionally, XooNET provides information on network properties of the Xoo interactome.

Conclusion
XooNET is an open and free public database server for protein interaction information for Xoo. It contains 4,538 proteins and 26,932 possible interactions consisting of 18,503 (PSIMAP), 3,118 (PEIMAP), and 8,938 (iPfam) pairs. In addition, XooNET provides 3,407 possible interaction pairs between two sets of proteins; 141 Xoo proteins that are predicted as membrane proteins and rice proteomes. The resultant interacting partners of a query protein can be easily retrieved by users as well as the interaction networks in graphical web interfaces. XooNET is freely available from http://bioportal.kobic.kr/XooNET/.
A dynamic Bayesian network approach to protein secondary structure prediction
Authors: Yao Xin-Qiu , Zhu Huaiqiu , She Zhen-Su 
Published: January 2008

Abstract

Background
Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant to sequence-structure relationship. However, at present, the prediction accuracy of pure HMM-type methods is much lower than that of machine learning-based methods such as neural networks (NN) or support vector machines (SVM).

Results
In this paper, we report a new method of probabilistic nature for protein secondary structure prediction, based on dynamic Bayesian networks (DBN). The new method models the PSI-BLAST profile of a protein sequence using a multivariate Gaussian distribution, and simultaneously takes into account the dependency between the profile and secondary structure and the dependency between profiles of neighboring residues. In addition, a segment length distribution is introduced for each secondary structure state. Tests show that the DBN method has made a significant improvement in the accuracy compared to other pure HMM-type methods. Further improvement is achieved by combining the DBN with an NN, a method called DBNN, which shows better Q
3 accuracy than many popular methods and is competitive to the current state-of-the-arts. The most interesting feature of DBN/DBNN is that a significant improvement in the prediction accuracy is achieved when combined with other methods by a simple consensus.

Conclusion
The DBN method using a Gaussian distribution for the PSI-BLAST profile and a high-ordered dependency between profiles of neighboring residues produces significantly better prediction accuracy than other HMM-type probabilistic methods. Owing to their different nature, the DBN and NN combine to form a more accurate method DBNN. Future improvement may be achieved by combining DBNN with a method of SVM type.