bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signature proteins that are distinctive of alpha proteobacteria
Authors: Kainth Pinay , Gupta Radhey S 
Published: June 2005

Abstract

Background
The alpha (α) proteobacteria, a very large and diverse group, are presently characterized solely on the basis of 16S rRNA trees, with no known molecular characteristic that is unique to this group. The genomes of three α-proteobacteria, Rickettsia prowazekii (RP), Caulobacter crescentus (CC) and Bartonella quintana (BQ), were analyzed in order to search for proteins that are unique to this group.

Results
Blast analyses of protein sequences from the above genomes have led to the identification of 61 proteins which are distinctive characteristics of α-proteobacteria and are generally not found in any other bacteria. These α-proteobacterial signature proteins are generally of hypothetical functions and they can be classified as follows: (i) Six proteins (CC2102, CC3292, CC3319, CC1887, CC1725 and CC1365) which are uniquely present in most sequenced α-proteobacterial genomes; (ii) Ten proteins (CC1211, CC1886, CC2245, CC3470, CC0520, CC0365, CC0366, CC1977, CC3010 and CC0100) which are present in all α-proteobacteria except the Rickettsiales; (iii) Five proteins (CC2345, CC3115, CC3401, CC3467 and CC1021) not found in the intracellular bacteria belonging to the order Rickettsiales and the Bartonellaceae family; (iv) Four proteins (CC1652, CC2247, CC3295 and CC1035) that are absent from various Rickettsiales as well as Rhodobacterales; (v) Three proteins (RP104, RP105 and RP106) that are unique to the order Rickettsiales and four proteins (RP766, RP192, RP030 and RP187) which are specific for the Rickettsiaceae family; (vi) Six proteins (BQ00140, BQ00720, BQ03880, BQ12030, BQ07670 and BQ11900) which are specific to the order Rhizobiales; (vii) Four proteins (BQ01660, BQ02450, BQ03770 and BQ13470) which are specific for the order Rhizobiales excluding the family Bradyrhizobiaceae; (viii) Nine proteins (BQ12190, BQ11460, BQ11450, BQ11430, BQ11380, BQ11160, BQ11120, BQ11100 and BQ11030 which are distinctive of the Bartonellaceae family;(ix) Six proteins (CC0189, CC0569, CC0331, CC0349, CC2323 and CC2637) which show sporadic distribution in α-proteobacteria, (x) Four proteins (CC2585, CC0226, CC2790 and RP382) in which lateral gene transfers are indicated to have occurred between α-proteobacteria and a limited number of other bacteria.

Conclusion
The identified proteins provide novel means for defining and identifying the α-proteobacteria and many of its subgroups in clear molecular terms and in understanding the evolution of this group of species. These signature proteins, together with the large number of α-proteobacteria specific indels that have recently been identified http://www.bacterialphylogeny.com, provide evidence that all species from this diverse group share many unifying and distinctive characteristics. Functional studies on these proteins should prove very helpful in the identification of such characteristics.
A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts
Authors: Galperin Michael Y 
Published: June 2005

Abstract

Background
Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.

Results
This paper presents results of a comprehensive census of signal transduction proteins – histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases – encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others.

Conclusion
The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the current leader Wolinella succinogenes, are found among the poorly studied beta-, delta- and epsilon-proteobacteria. Among all bacterial phyla, only cyanobacteria appear to be true introverts, probably due to their capacity to conduct oxygenic photosynthesis, using a complex system of intracellular membranes. The census data, available at http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html, can be used to get an insight into metabolic and behavioral propensities of each given organism and improve prediction of the organism's properties based solely on its genome sequence.
A systematic review of how homeopathy is represented in conventional and CAM peer reviewed journals
Authors: Caulfield Timothy , DeBow Suzanne 
Published: June 2005

Abstract

Background
Growing popularity of complementary and alternative medicine (CAM) in the public sector is reflected in the scientific community by an increased number of research articles assessing its therapeutic effects. Some suggest that publication biases occur in mainstream medicine, and may also occur in CAM. Homeopathy is one of the most widespread and most controversial forms of CAM. The purpose of this study was to compare the representation of homeopathic clinical trials published in traditional science and CAM journals.

Methods
Literature searches were performed using Medline (PubMed), AMED and Embase computer databases. Search terms included "homeo-pathy, -path, and -pathic" and "clinical" and "trial". All articles published in English over the past 10 years were included. Our search yielded 251 articles overall, of which 46 systematically examined the efficacy of homeopathic treatment. We categorized the overall results of each paper as having either "positive" or "negative" outcomes depending upon the reported effects of homeopathy. We also examined and compared 15 meta-analyses and review articles on homeopathy to ensure our collection of clinical trials was reasonably comprehensive. These articles were found by inserting the term "review" instead of "clinical" and "trial".

Results
Forty-six peer-reviewed articles published in a total of 23 different journals were compared (26 in CAM journals and 20 in conventional journals). Of those in conventional journals, 69% reported negative findings compared to only 30% in CAM journals. Very few articles were found to be presented in a "negative" tone, and most were presented using "neutral" or unbiased language.

Conclusion
A considerable difference exists between the number of clinical trials showing positive results published in CAM journals compared with traditional journals. We found only 30% of those articles published in CAM journals presented negative findings, whereas over twice that amount were published in traditional journals. These results suggest a publication bias against homeopathy exists in mainstream journals. Conversely, the same type of publication bias does not appear to exist between review and meta-analysis articles published in the two types of journals.
Manuscript Architect: a Web application for scientific writing in virtual interdisciplinary groups
Authors: Pietrobon Ricardo , Nielsen Karen C , Steele Susan M , Menezes Andreia P , Martins Henrique , Jacobs Danny O 
Published: June 2005

AbstractBackgroundAlthough scientific writing plays a central role in the communication of clinical research findings and consumes a significant amount of time from clinical researchers, few Web applications have been designed to systematically improve the writing process.This application had as its main objective the separation of the multiple tasks associated with scientific writing into smaller components. It was also aimed at providing a mechanism where sections of the manuscript (text blocks) could be assigned to different specialists. Manuscript Architect was built using Java language in conjunction with the classic lifecycle development method. The interface was designed for simplicity and economy of movements. Manuscripts are divided into multiple text blocks that can be assigned to different co-authors by the first author. Each text block contains notes to guide co-authors regarding the central focus of each text block, previous examples, and an additional field for translation when the initial text is written in a language different from the one used by the target journal. Usability was evaluated using formal usability tests and field observations.ResultsThe application presented excellent usability and integration with the regular writing habits of experienced researchers. Workshops were developed to train novice researchers, presenting an accelerated learning curve. The application has been used in over 20 different scientific articles and grant proposals.ConclusionThe current version of Manuscript Architect has proven to be very useful in the writing of multiple scientific texts, suggesting that virtual writing by interdisciplinary groups is an effective manner of scientific writing when interdisciplinary work is required.
Delayed polarization of mononuclear phagocyte transcriptional program by type I interferon isoforms
Authors: Stroncek David F , Basil Christopher , Nagorsen Dirk , Deola Sara , Aricó Eleonora , Smith Kina , Wang Ena , Marincola Francesco M , Panelli Monica C 
Published: June 2005

AbstractBackgroundInterferon (IFN)-α is considered a key modulator of immunopathological processes through a signature-specific activation of mononuclear phagocytes (MPs). This study utilized global transcript analysis to characterize the effects of the entire type I IFN family in comparison to a broad panel of other cytokines on MP previously exposed to Lipopolysaccharide (LPS) stimulation in vitro.ResultsImmature peripheral blood CD14+ MPs were stimulated with LPS and 1 hour later with 42 separate soluble factors including cytokines, chemokines, interleukins, growth factors and IFNs. Gene expression profiling of MPs was analyzed 4 and 9 hours after cytokine stimulation. Four hours after stimulation, the transcriptional analysis of MPs revealed two main classes of cytokines: one associated with the alternative and the other with the classical pathway of MP activation without a clear polarization of type I IFNs effects. In contrast, after 9 hours of stimulation most type I IFN isoforms induced a characteristic and unique transcriptional pattern separate from other cytokines. These "signature" IFNs included; IFN-β, IFN-α2b/α2, IFN-αI, IFN-α2, IFN-αC, IFN-αJ1, IFN-αH2, and INF-α4B and induced the over-expression of 44 genes, all of which had known functional relationships with IFN such as myxovirus resistance (Mx)-1, Mx-2, and interferon-induced hepatitis C-associated microtubular aggregation protein. A second group of type I IFNs segregated separately and in closer association with the type II IFN-γ. The phylogenetic relationship of amino acid sequences among type I IFNs did not explain their sub-classification, although differences at positions 94 through 109 and 175 through 189 were present between the signature and other IFNs.ConclusionSeven IFN-α isoforms and IFN-β participate in the late phase polarization of MPs conditioned by LPS. This information broadens the previous view of the central role played by IFN-α in autoimmunity and tumor rejection by including and/or excluding an array of related factors likely to be heterogeneously expressed by distinct sub-populations of individuals in sickness or in response to biological therapy.
A new journal – "Theoretical Biology and Medical Modelling"
Authors: Wheatley Denys N 
Published: June 2005

Abstract
Biology has a conceptual basis that allows one to build models and theorize across many life sciences, including medicine and medically-related disciplines. A dearth of good venues for publication has been perceived during a period when bioinformatics, systems analysis and biomathematics are burgeoning.
Steps have been taken to provide the sort of journal with a quick turnaround time for manuscripts which is online and freely accessible to all readers, whatever their persuasion or discipline. We have now been running for some time a journal which has had many good papers presented pre-launch, and a steady stream of papers thereafter. The value of this journal as a new venue has already been vindicated.
Within a short space of time, we have founded a state-of-the-art electronic journal freely accessible to all in a much sort-after interdisciplinary field that will be of benefit to the thinking life scientist, which must include medically qualified doctors as well as scientists who prefer to build their new hypotheses on basic principles and sound concepts underpinning biology. At the same time, these principles are not sacrosanct and require critical analysis. The journal http://www.tbiomed.com promises to deliver many exciting ideas in the future.
Antibodies to citrullinated proteins and differences in clinical progression of rheumatoid arthritis
Authors: van der Helm-van Mil Annette HM , Verpoort Kirsten N , Breedveld Ferdinand C , Toes René EM , Huizinga Tom WJ 
Published: June 2005

AbstractAntibodies to citrullinated proteins (anti-cyclic-citrullinated peptide [anti-CCP] antibodies) are highly specific for rheumatoid arthritis (RA) and precede the onset of disease symptoms, indicating a pathogenetic role for these antibodies in RA. We recently showed that distinct genetic risk factors are associated with either anti-CCP-positive disease or anti-CCP-negative disease. These data are important as they indicate that distinct pathogenic mechanisms are underlying anti-CCP-positive disease or anti-CCP-negative disease. Likewise, these observations raise the question of whether anti-CCP-positive RA and anti-CCP-negative RA are clinically different disease entities. We therefore investigated whether RA patients with anti-CCP antibodies have a different clinical presentation and disease course compared with patients without these autoantibodies. In a cohort of 454 incident patients with RA, 228 patients were anti-CCP-positive and 226 patients were anti-CCP-negative. The early symptoms, tender and swollen joint count, and C-reactive protein level at inclusion, as well as the swollen joint count and radiological destruction during 4 years of follow-up, were compared for the two groups. There were no differences in morning stiffness, type, location and distribution of early symptoms, patients' rated disease activity and C-reactive protein at inclusion between RA patients with and without anti-CCP antibodies. The mean tender and swollen joint count for the different joints at inclusion was similar. At follow-up, patients with anti-CCP antibodies had more swollen joints and more severe radiological destruction. Nevertheless, the distribution of affected joints, for swelling, bone erosions and joint space narrowing, was similar. In conclusion, the phenotype of RA patients with or without anti-CCP antibodies is similar with respect to clinical presentation but differs with respect to disease course.
Modulation of monocyte matrix metalloproteinase-2 by breast adenocarcinoma cells
Authors: Szabo Kristina A , Singh Gurmit 
Published: June 2005

Abstract
Introduction
The presence of monocyte and macrophage cells in growing breast tumors, and the positive relationship between the degree of immune cell infiltration and tumor growth, suggest a possible paracrine growth regulatory function of immune cells in breast cancer.

Method
To better understand the interaction between monocytes and breast cancer cells, in vitro matrix metalloproteinase and tissue inhibitor of metalloproteinase activity was assessed from the THP-1 myeloid cell line in response to conditioned media from two breast cancer cell lines, MCF-7 and MDA-MB-231.

Results
Enzymography and immunoblotting revealed increased MMP-2 as well as increased levels of TIMP-1 and TIMP-2. Furthermore, a significant increase in the invasive potential of MCF-7 and MDA-MB-231 cells was noted in response to THP-1 cell-conditioned media.

Conclusion
These data demonstrate that monocyte cells in the breast tumor microenvironment play an important role in the modulation of MMPs, which may have a significant effect on the control of tumor growth and metastatic spread.
Association between β2-glycoprotein I gene polymorphisms and pediatric SLE and antiphospholipid antibodies
Authors: von Scheven E , Elder M E 
Published: June 2005

Antibodies against phospholipids (PL) and PL-binding proteins have been causally implicated in antiphospholipid syndrome (APS). Mutations in the fifth domain of the β2-glycoprotein I (β2GPI) protein, a putative PL-binding site, may play a critical role in APS pathogenesis. The purpose of this study was to identify associations between β2GPI mutations and both antiphospholipid antibodies (aPL) and their associated clinical manifestations in a pediatric and adolescent cohort and to search for novel mutations. Genetic analysis of β2GPI was performed in 58 youths with systemic lupus erythematosus (SLE) and/or aPL, to identify known polymorphisms at amino acids 247 and 306 as well as novel mutations in exon 7 of the β2GPI gene, and their association with aPL-associated clinical manifestations. Our results demonstrate an association between substitution of Val for Leu at AA247 (L247V) of β2GPI and both the development of aPL (P = 0.05) and aPL-associated clinical manifestations (P = 0.03) among pediatric patients. The odds ratio associated with risk of aPL-associated clinical manifestations for the homozygous VV polymorphism was 5.5 (CI 1.3-23, P = 0.03) for the overall cohort, and 4.75 (CI 0.66-55.49, P = 0.06) after adjusting for ethnicity. The association was not significant after stratifying for SLE versus non-SLE. Association between the VV genotype at amino acid 247 of β2GPI and clinical disease supports a genetic cause for APS among children and adolescents. Neither novel exon 7 β2GPI mutations or the previously described C306G polymorphism was identified in this pediatric cohort.
Intratracheal budesonide-poly (lactide-co-glycolide) microparticles reduce oxidative stress, VEGF expression, and vascular leakage in a benzo(a)pyrene-fed mouse model
Authors: Bandi Nagesh , Ayalasomayajula Surya P , Dhanda Devender S , Iwakawa Jun , Cheng Pi-Wan , Kompella Uday B 
Published: June 2005

Abstract
The purpose of this study was to determine whether intratracheally instilled polymeric budesonide microparticles could sustain lung budesonide levels for one week and inhibit early biochemical changes associated with benzo(a)pyrene (B[a]P) feeding in a mouse model for lung tumours. Polymeric microparticles of budesonide-poly (dl-lactide-co-glycolide) (PLGA 50:50) were prepared using a solvent evaporation technique and characterized for their size, morphology, encapsulation efficiency, and in-vitro release. The microparticles were administered intratracheally (i.t.) to B[a]P-fed A/J mice. At the end of one week drug levels in the lung tissue and bronchoalveolar lavage (BAL) were estimated using HPLC and compared with systemic (intramuscular) administration. In addition, in-vivo end points including malondialdehyde (MDA), glutathione (GSH), total protein levels and vascular endothelial growth factor (VEGF) in BAL, and VEGF and c-myc mRNA levels in the lung tissue were assessed at the end of one week following intratracheal administration of budesonide microparticles. Budesonide-PLGA microparticles (1–2 μm), with a budesonide loading efficiency of 69–94%, sustained in-vitro budesonide release for over 21 days. Compared with the intramuscular route, intratracheally administered budesonide-PLGA microparticles resulted in higher budesonide levels in the BAL and lung tissue. In-vivo, B[a]P-feeding increased BAL MDA, lung VEGF mRNA, lung c-myc mRNA, BAL total protein, and BAL VEGF levels by 60, 112, 71, 154, and 78%, respectively, and decreased BAL GSH by 62%. Interestingly, intratracheally administered budesonide-PLGA particles inhibited these biochemical changes. Thus, biodegradable budesonide microparticles sustained budesonide release and reduced MDA accumulation, GSH depletion, vascular leakage, and VEGF and c-myc expression in B[a]P-fed mice, indicating the potential of locally delivered sustained-release particles for inhibiting angiogenic factors in lung cancer.
Design and evaluation of compound metformin/glipizide elementary osmotic pump tablets
Authors: Ouyang Defang , Nie Shufang , Li Wei , Guo Hong , Liu Hui , Pan Weisan 
Published: June 2005

Abstract
A simple elementary osmotic pump (EOP) system that could deliver metformin hydrochloride (MT) and glipizide (GZ) simultaneously for extended periods of time was developed in order to reduce the problems associated with multidrug therapy of type 2 non-insulin-dependent diabetes mellitus. In general, both highly and poorly water-soluble drugs are not good candidates for elementary osmotic delivery. However, MT is a highly soluble drug with a high dose (500 mg) while GZ is a water-insoluble drug with a low dose (5 mg) so it is a great challenge to pharmacists to provide satisfactory extended release of MT and GZ. In this paper sodium carbonate was used to modulate the solubility of GZ within the core and MT was not only one of the active ingredients but also the osmotic agent. The optimal EOP was found to deliver both drugs at a rate of approximately zero order for up to 10h in pH 6.8, independent of environment media. In-vivo evaluation was performed relative to the equivalent dose of conventional MT tablet and GZ tablet by a cross-study in six Beagle dogs. The EOP had a good sustained effect in comparison with the conventional product. The prototype design of the system could be applied to other combinations of drugs used for cardiovascular diseases, diabetes, etc.
In-vitro antiproliferative effects on human tumour cell lines of extracts and jacaranone from Senecio leucanthemifolius Poiret
Authors: Loizzo M R , Tundis R , Statti G A , Menichini F , Houghton P J 
Published: June 2005

Abstract
We have studied the cytotoxic activity of extracts and jacaranone from Senecio leucanthemifolius Poiret. Extracts from S. leucanthemifolius were able to inhibit the in-vitro proliferation of a series of human tumour cell lines. The dichloromethane extract demonstrated effective cytotoxic activity with an IC50 of 20.1 μg mL−1 on the large cell carcinoma cell line COR-L23. The ethyl acetate extract showed an IC50 value of 5.0 μg mL−1 and the butanol extract an IC50 value of 6.4 μg mL−1 on the same cell line. A major active constituent of the dichloromethane extract was shown to be jacaranone, which was demonstrated to have a very strong activity against all of the tumour cell lines with IC50 values between 2.86 and 3.85 μg mL−1, although it did not account for all the activity observed. Constituents of S. leucanthemifolius extracts were identified by GC/MS analysis and NMR.