bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of endothelial thrombomodulin expression by inflammatory cytokines is mediated by activation of nuclear factor-kappa B
Authors: Sohn Richard H. , Deming Clayton B. , Johns David C. , Champion Hunter C. , Bian Ce , Gardner Kevin , Rade Jeffrey J. 
Published: January 2005

AbstractInflammation and thrombosis are increasingly recognized as interrelated biologic processes. Endothelial cell expression of thrombomodulin (TM), a key component of the anticoagulant protein C pathway, is potently inhibited by inflammatory cytokines. Because the mechanism underlying this effect is largely unknown, we investigated a potential role for the inflammatory transcription factor nuclear factor-kappa B (NF-κB). Blocking NF-κB activation effectively prevented cytokine-induced down-regulation of TM, both in vitro and in a mouse model of tumor necrosis factor-α (TNF-α)–mediated lung injury. Although the TM promoter lacks a classic NF-κB consensus site, it does contain tandem Ets transcription factor binding sites previously shown to be important for both constitutive TM gene expression and cytokine-induced repression. Using electrophoretic mobility shift assay and chromatin immunoprecipitation, we found that multiple Ets species bind to the TNF-α response element within the TM promoter. Although cytokine exposure did not alter Ets factor binding, it did reduce binding of p300, a coactivator required by Ets for full transcriptional activity. Overexpression of p300 also prevented TM repression by cytokines. We conclude that NF-κB is a critical mediator of TM repression by cytokines. Further evidence suggests a mechanism involving competition by NF-κB for limited pools of the transcriptional coactivator p300 necessary for TM gene expression.
Induction of polyploidization in leukemic cell lines and primary bone marrow by Src kinase inhibitor SU6656
Authors: Lannutti Brian J. , Blake Noel , Gandhi Manish J. , Reems Jo Anna , Drachman Jonathan G. 
Published: January 2005

AbstractMegakaryocytes (MKs) undergo successive rounds of endomitosis during differentiation, resulting in polyploidy (typically, 16-64N). Previous studies have demonstrated that this occurs through an interruption of normal cell cycle progression during anaphase. However, the molecular mechanism(s) controlling this unique process is undefined. In the present report, we examine the effect of an Src kinase inhibitor, SU6656, on thrombopoietin (TPO)-induced growth and differentiation. Remarkably, when SU6656 (2.5 μM) was added to a megakaryocytic cell line, UT-7/TPO, the cells ceased cell division but continued to accumulate DNA by endomitosis. During this interval, CD41 and CD61 expression on the cell surface increased. Similar effects on polyploidization and MK differentiation were seen with expanded primary MKs, bone marrow from 2 patients with myelodysplastic syndrome, and other cell lines with MK potential. Our data suggest that SU6656 might be useful as a differentiation-inducing agent for MKs and is an important tool for understanding the molecular basis of MK endomitosis.
Autocrine- and paracrine-activated receptor tyrosine kinases in classic Hodgkin lymphoma
Authors: Renné Christoph , Willenbrock Klaus , Küppers Ralf , Hansmann Martin-Leo , Bräuninger Andreas 
Published: January 2005

AbstractThe pathogenesis of Hodgkin lymphoma (HL) is still largely unknown. Based on a search for footprints of pathogenetic mechanisms in global RNA expression data of Hodgkin/Reed-Sternberg (HRS) cell lines, we analyzed the expression and activation of 6 receptor tyrosine kinases (RTKs) in classic HL. Immunohistochemistry revealed that the RTKs platelet-derived growth factor receptor A (PDGFRA), DDR2, EPHB1, RON, TRKB, and TRKA were each expressed in HRS cells in 30% to 75% of patients. These RTKs were not expressed in normal B cells, the origin of HRS cells, or in most B-cell non-Hodgkin lymphoma (NHL). In the majority of patients at least one RTK was expressed, and in most patients several RTKs were coexpressed, most prominently in Hodgkin lymphoma of the nodular sclerosis subtype. Phosphotyrosine-specific antibodies revealed exemplarily the activation of PDGFRA and TRKA/B and an elevation of cellular phosphotyrosine content. Immunohistochemistry for RTK ligands indicated that DDR2 and TRKA are likely activated in a paracrine fashion, whereas PDGFRA and EPHB1 seem to be activated by autocrine loops. Activating mutations were not detected in cDNA encoding the RTKs in HRS cell lines. These findings show the unprecedented coexpression of multiple RTKs in a tumor and indicate that aberrant RTK signaling is an important factor in HL pathogenesis and that it may be a novel therapeutic target.
Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate α-galactosidase and α-N-acetylgalactosaminidase
Authors: Hujová Jana , Sikora Jakub , Dobrovolný Robert , Poupětová Helena , Ledvinová Jana , Kostrouchová Marta , Hřebíček Martin 
Published: January 2005

Abstract
Background
Human α-galactosidase A (α-GAL) and α-N-acetylgalactosaminidase (α-NAGA) are presumed to share a common ancestor. Deficiencies of these enzymes cause two well-characterized human lysosomal storage disorders (LSD) – Fabry (α-GAL deficiency) and Schindler (α-NAGA deficiency) diseases. Caenorhabditis elegans was previously shown to be a relevant model organism for several late endosomal/lysosomal membrane proteins associated with LSDs. The aim of this study was to identify and characterize C. elegans orthologs to both human lysosomal luminal proteins α-GAL and α-NAGA.

Results
BlastP searches for orthologs of human α-GAL and α-NAGA revealed a single C. elegans gene (R07B7.11) with homology to both human genes (α-ga lactosidase and α-N-a cetylgalactosaminidase) – gana-1. We cloned and sequenced the complete gana-1 cDNA and elucidated the gene organization.
Phylogenetic analyses and homology modeling of GANA-1 based on the 3D structure of chicken α-NAGA, rice α-GAL and human α-GAL suggest a close evolutionary relationship of GANA-1 to both human α-GAL and α-NAGA.
Both α-GAL and α-NAGA enzymatic activities were detected in C. elegans mixed culture homogenates. However, α-GAL activity on an artificial substrate was completely inhibited by the α-NAGA inhibitor, N-acetyl-D-galactosamine.
A GANA-1:: GFP fusion protein expressed from a transgene, containing the complete gana-1 coding region and 3 kb of its hypothetical promoter, was not detectable under the standard laboratory conditions. The GFP signal was observed solely in a vesicular compartment of coelomocytes of the animals treated with Concanamycin A (CON A) or NH4Cl, agents that increase the pH of the cellular acidic compartment.
Immunofluorescence detection of the fusion protein using polyclonal anti-GFP antibody showed a broader and coarsely granular cytoplasmic expression pattern in body wall muscle cells, intestinal cells, and a vesicular compartment of coelomocytes.
Inhibition of gana-1 by RNA interference resulted in a decrease of both α-GAL and α-NAGA activities measured in mixed stage culture homogenates but did not cause any obvious phenotype.

Conclusions
GANA-1 is a single C. elegans ortholog of both human α-GAL and α-NAGA proteins. Phylogenetic, homology modeling, biochemical and GFP expression analyses support the hypothesis that GANA-1 has dual enzymatic activity and is localized in an acidic cellular compartment.
CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences
Authors: Guryev Victor , Berezikov Eugene , Cuppen Edwin 
Published: January 2005

Abstract
Background
With the recent progress made in large-scale genome sequencing projects a vast amount of novel data is becoming available. A comparative sequence analysis, exploiting sequence information from various resources, can be used to uncover hidden information, such as genetic variation. Although there are enormous amounts of SNPs for a wide variety of organisms submitted to NCBI dbSNP and annotated in most genome assembly viewers like Ensembl and the UCSC Genome Browser, these platforms do not easily allow for extensive annotation and incorporation of experimental data supporting the polymorphism. However, such information is very important for selecting the most promising and useful candidate polymorphisms for use in experimental setups.

Description
The CASCAD database is designed for presentation and query of candidate SNPs that are retrieved by in silico mining of high-throughput sequencing data. Currently, the database provides collections of laboratory rat (Rattus norvegicus) and zebrafish (Danio rerio) candidate SNPs. The database stores detailed information about raw data supporting the candidate, extensive annotation and links to external databases (e.g. GenBank, Ensembl, UniGene, and LocusLink), verification information, and predictions of a potential effect for non-synonymous polymorphisms in coding regions. The CASCAD website allows search based on an arbitrary combination of 27 different parameters related to characteristics like candidate SNP quality, genomic localization, and sequence data source or strain. In addition, the database can be queried with any custom nucleotide sequences of interest. The interface is crosslinked to other public databases and tightly coupled with primer design and local genome assembly interfaces in order to facilitate experimental verification of candidates.

Conclusions
The CASCAD database discloses detailed information on rat and zebrafish candidate SNPs, including the raw data underlying its discovery. An advanced web-based search interface http://cascad.niob.knaw.nl allows universal access to the database content and allows various queries supporting many types of research utilizing single nucleotide polymorphisms.
FAM20: an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells
Authors: Nalbant Demet , Youn Hyewon , Nalbant S Isil , Sharma Savitha , Cobos Everardo , Beale Elmus G , Du Yang , Williams Simon C 
Published: January 2005

Abstract
Background
Hematopoiesis is a complex developmental process controlled by a large number of factors that regulate stem cell renewal, lineage commitment and differentiation. Secreted proteins, including the hematopoietic growth factors, play critical roles in these processes and have important biological and clinical significance. We have employed representational difference analysis to identify genes that are differentially expressed during experimentally induced myeloid differentiation in the murine EML hematopoietic stem cell line.

Results
One identified clone encoded a previously unidentified protein of 541 amino acids that contains an amino terminal signal sequence but no other characterized domains. This protein is a member of family of related proteins that has been named family with sequence similarity 20 (FAM20) with three members (FAM20A, FAM20B and FAM20C) in mammals. Evolutionary comparisons revealed the existence of a single FAM20 gene in the simple vertebrate Ciona intestinalis and the invertebrate worm Caenorhabditis elegans and two genes in two insect species, Drosophila melanogaster and Anopheles gambiae. Six FAM20 family members were identified in the genome of the pufferfish, Fugu rubripes and five members in the zebrafish, Danio rerio. The mouse Fam20a protein was ectopically expressed in a mammalian cell line and found to be a bona fide secreted protein and efficient secretion was dependent on the integrity of the signal sequence. Expression analysis revealed that the Fam20a gene was indeed differentially expressed during hematopoietic differentiation and that the other two family members (Fam20b and Fam20c) were also expressed during hematcpoiesis but that their mRNA levels did not vary significantly. Likewise FAM20A was expressed in more limited set of human tissues than the other two family members.

Conclusions
The FAM20 family represents a new family of secreted proteins with potential functions in regulating differentiation and function of hematopoietic and other tissues. The Fam20a mRNA was only expressed during early stages of hematopoietic development and may play a role in lineage commitment or proliferation. The expansion in gene number in different species suggests that the family has evolved as a result of several gene duplication events that have occurred in both vertebrates and invertebrates.
Half versus full vacuum suction drainage after modified radical mastectomy for breast cancer- a prospective randomized clinical trial[ISRCTN24484328]
Authors: Chintamani  , Singhal Vinay , Singh JP , Bansal Anju , Saxena Sunita 
Published: January 2005

Abstract
Background
Suction drains are routinely used after modified radical mastectomy and are an important factor contributing to increased hospital stay as the patients are often discharged only after their removal. Amongst various factors that influence the amount of postoperative drainage, the negative suction pressure applied to the drain has been reported to be of great significance. While a high negative suction pressure is expected to drain the collection and reduce the dead space promptly, it may also prevent the leaking lymphatics from closing and lead to increased drainage from the wound. Against this background a prospective randomized clinical study was conducted to compare the amount and duration of drainage between a half negative suction and full vacuum suction drainage in patients following modified radical mastectomy. The associated postoperative morbidity was also compared between the two groups.

Methods
85 FNAC (fine needle aspiration cytology) proven cases of locally advanced breast cancer were randomized. (Using randomly ordered sealed envelops, which were opened immediately before the closure of the wound) in to 50 patients with full vacuum suction (pressure = 700 g/m2) and 35 cases in to half vacuum suction drainage (pressure = 350 g/m2) groups. The two groups were comparable in respect of age, weight, and technique of operation and extent of axillary dissection. Surgery was performed by the same surgical team comprising of five surgeons (two senior and three resident surgeons) using a standardized technique with electrocautery. External compression dressing was provided over the axilla for first 48 hrs and following that patients were encouraged to do active and passive shoulder exercises. The outcomes measured were postoperative morbidity and the length of hospital stay.
Statistical methods used: Descriptive studies were performed with SPSS version 10 and group characteristics were compared using student t-test.

Results
Half vacuum suction drains were removed earlier than the full suction vacuum suction drains. There was no significant difference in the incidence of seroma formation in the two groups and there was a significant reduction in the total hospital stay in patients with half vacuum suction drainage systems as compared to the full suction drainage group (p < 0.001) without any added morbidity.

Conclusions
Half negative suction drains provide an effective compromise between no suction and full or high suction drainage after modified radical mastectomy by reducing the hospital stay and the post operative morbidity including post operative seromas.
The importance of socio-economic context for social marketing models for improving reproductive health: Evidence from 555 years of program experience
Authors: Meekers Dominique , Rahaim Stephen 
Published: January 2005

Abstract
Background
Over the past two decades, social marketing programs have become an important element of the national family planning and HIV prevention strategy in several developing countries. As yet, there has not been any comprehensive empirical assessment to determine which of several social marketing models is most effective for a given socio-economic context. Such an assessment is urgently needed to inform the design of future social marketing programs, and to avoid that programs are designed using an ineffective model.

Methods
This study addresses this issue using a database of annual statistics about reproductive health oriented social marketing programs in over 70 countries. In total, the database covers 555 years of program experience with social marketing programs that distribute and promote the use of oral contraceptives and condoms. Specifically, our analysis assesses to what extent the model used by different reproductive health social marketing programs has varied across different socio-economic contexts. We then use random effects regression to test in which socio-economic context each of the models is most successful at increasing use of socially marketed oral contraceptives and condoms.

Results
The results show that there has been a tendency to design reproductive health social marketing program with a management structure that matches the local context. However, the evidence also shows that this has not always been the case. While socio-economic context clearly influences the effectiveness of some of the social marketing models, program maturity and the size of the target population appear equally important.

Conclusions
To maximize the effectiveness of future social marketing programs, it is essential that more effort is devoted to ensuring that such programs are designed using the model or approach that is most suitable for the local context.
Use of email for patient communication in student health care: a cross-sectional study
Authors: Castrén Johanna , Niemi Marja , Virjo Irma 
Published: January 2005

Abstract
Background
Citizens increasingly use email in personal communication. It is not however clear to what extent physicians utilize it for patient communication. Our study was designed to examine physicians' activity in using email and to estimate the proportion of email messages missing from documentation in electronic patient records (EPR).

Methods
All physicians (n = 76; 48 general practitioners and 28 specialists) at the Finnish Student Health Service received a questionnaire by email, and were asked to print it and keep a daily tally of visits, phone calls and email messages over the study period of one working week (5.5. – 9.5.2003). The response rate was 70%. The data originating from the questionnaire were compared with statistical data from the EPR during the study period.

Results
The majority (79%, 41/52) of doctors reported using email with patients, averaging 8.6 (range: 0–96) email contacts and a percentage rate of "email / visit" 20% (range: 0–185%) in one working week. Doctors in the capital city region and those doctors who had a positive attitude toward email for patient communication were most active in email use. Up to 73% of email contacts were not documented in the EPR.

Conclusion
The activity in using email with patients verified among Finnish physicians is compatible with recent study results elsewhere. The notable proportion of un-recorded email messages establishes the need for an electric communication system built into the EPR to improve the quality of patient care and to limit medico-legal risks.
Clinical response in Japanese metastatic melanoma patients treated with peptide cocktail-pulsed dendritic cells
Authors: Akiyama Yasuto , Tanosaki Ryuji , Inoue Naoki , Shimada Makiko , Hotate Yukie , Yamamoto Akifumi , Yamazaki Naoya , Kawashima Ichiro , Nukaya Ikuei , Takesako Kazutoh , Maruyama Kouji , Takaue Yoichi , Yamaguchi Ken 
Published: January 2005

Abstract
Background
Metastatic, chemotherapy-resistant melanoma is an intractable cancer with a very poor prognosis. As to immunotherapy targeting metastatic melanoma, HLA-A2+ patients were mainly enrolled in the study in Western countries. However, HLA-A24+ melanoma patients-oriented immunotherapy has not been fully investigated. In the present study, we investigated the effect of dendritic cell (DC)-based immunotherapy on metastatic melanoma patients with HLA-A2 or A24 genotype.

Methods
Nine cases of metastatic melanoma were enrolled into a phase I study of monocyte-derived dendritic cell (DC)-based immunotherapy. HLA-genotype analysis revealed 4 cases of HLA-A*0201, 1 of A*0206 and 4 of A*2402. Enriched monocytes were obtained using OptiPrep™ from leukapheresis products, and then incubated with GM-CSF and IL-4 in a closed serum-free system. After pulsing with a cocktail of 5 melanoma-associated synthetic peptides (gp100, tyrosinase, MAGE-2, MAGE-3 and MART-1 or MAGE-1) restricted to HLA-A2 or A24 and KLH, cells were cryopreserved until used. Finally, thawed DCs were washed and injected subcutaneously (s.c.) into the inguinal region in a dose-escalation manner.

Results
The mean percentage of DCs rated as lin-HLA-DR+ in melanoma patients was 46.4 ± 15.6 %. Most of DCs expressed high level of co-stimulatory molecules and type1 phenotype (CD11c+HLA-DR+), while a moderate number of mature DCs with CD83 and CCR7 positive were contained in DC products. DC injections were well tolerated except for transient liver dysfunction (elevation of transaminases, Grade I-II). All 6 evaluable cases except for early PD showed positive immunological responses to more than 2 melanoma peptides in an ELISPOT assay. Two representative responders demonstrated strong HLA-class I protein expression in the tumor and very high scores of ELISPOT that might correlate to the regression of metastatic tumors. Clinical response through DC injections was as follows : 1CR, 1 PR, 1SD and 6 PD. All 59 DC injections in the phase I study were tolerable in terms of safety, however, the maximal tolerable dose of DCs was not determined.

Conclusions
These results suggested that peptide cocktail-treated DC-based immunotherapy had the potential for utilizing as one of therapeutic tools against metastatic melanoma in Japan.
Ingested Medium-Chain Fatty Acids Are Directly Utilized for the Acyl Modification of Ghrelin
Authors: Nishi Yoshihiro , Hiejima Hiroshi , Hosoda Hiroshi , Kaiya Hiroyuki , Mori Kenji , Fukue Yoshihiko , Yanase Toshihiko , Nawata Hajime , Kangawa Kenji , Kojima Masayasu 
Published: January 2005

AbstractGhrelin, an acylated brain and gut peptide, is primarily produced by endocrine cells of the gastric mucosa for secretion into the circulation. The major active form of ghrelin is a 28-amino-acid peptide containing an n-octanoyl modification at serine that is essential for activity. Studies have identified multiple physiological functions for ghrelin, including GH release, appetite stimulation, and metabolic fuel preference. Until now, there has not been any report detailing the mechanism of ghrelin acyl modification. Here we report that ingestion of either medium-chain fatty acids (MCFAs) or medium-chain triacylglycerols (MCTs) increased the stomach concentrations of acylated ghrelin without changing the total (acyl- and des-acyl-) ghrelin amounts. After ingestion of either MCFAs or MCTs, the carbon chain lengths of the acyl groups attached to nascent ghrelin molecules corresponded to that of the ingested MCFAs or MCTs. Ghrelin peptides modified with n-butyryl or n-palmitoyl groups, however, could not be detected after ingestion of the corresponding short-chain or long-chain fatty acids, respectively. Moreover, n-heptanoyl ghrelin, an unnatural form of ghrelin, could be detected in the stomach of mice after ingestion of either n-heptanoic acid or glyceryl triheptanoate. These findings indicate that ingested medium-chain fatty acids are directly used for the acylation of ghrelin.