bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal storing histiocytosis of the skin associated with multiple myeloma
Authors: Pock Lumír , Stuchlík David , Hercogová Jana 
Published: April 2006

AbstractBackground  Crystal storing histiocytosis (CSH) imitating rhabdomyom is a very rare disease entity involving different tissues. The skin is involved in extremely rare cases.Objectives  To describe the clinical and histopathological characteristics in a patient with unusually extensive skin involvement.Observations  A 62‐year‐old woman presented with a large red infiltrated verrucosus lesion on the anterior aspect of the chest and on the neck. The skin biopsy revealed histiocytes throughout the whole dermis containing thin crystaloid structures in the cytoplasm. Upon histopathological examination, crystal‐storing histiocytosis was diagnosed and consequently a hematological examination revealed multiple myeloma IgG Kappa. Skin involvement by CSH proceeded the diagnosis of multiple myeloma by 4 years.Conclusions  Phagocytosis of crystals of immunoglobulins by histiocytes (crystals storing histiocytosis) is a rare symptom associated most often with lymphoproliferative disease. The clinical picture is not characteristic, in the histopathologic picture it is striking similarity to rhabdomyom. The skin involvement by crystal storing histiocytosis can be the first symptom of malignant lymphoma that can proceed the hematological malignancy by years.
Increased capacity for axonal outgrowth using xenogenic tissue in vitro and in a rodent model of Parkinson's disease
Authors: Kuan Wei‐Li , Hurelbrink Carrie B , Barker Roger A. 
Published: April 2006

Kuan W‐L, Hurelbrink CB, Barker RA. Increased capacity for axonal outgrowth using xenogenic tissue in vitro and in a rodent model of Parkinson's disease. Xenotransplantation 2006; 13: 233–247. © Blackwell Munksgaard, 2006Abstract:  Background:  It has previously been proposed that grafted neurons may have the potential for more extensive axonal outgrowth in a xenogenic environment, and may thus possess a primary advantage over allografts in central nervous system repair and circuit reconstruction. In order to directly address this issue, fibre outgrowth from primary dopaminergic neurons was examined both in vitro and in vivo in an allogenic or xenogenic environment. A combination of species was used to circumvent problems relating to different gestational/developmental periods for such cells.Methods:  In the in vitro experiments, axon length was measured over 2 to 14 days in cultures derived from either rat or mouse ventral mesencephalon (VM) tissue co‐cultured onto either a monolayer of the rat Neu7 inhibitory cell line or fetal rodent cortical tissue. In the in vivo experiments, fetal rat or mouse VM tissue was transplanted into the striatum or substantia nigra of 6‐hydroxydopamine‐lesioned athymic rats. Amphetamine‐induced rotations were observed for 3 months post‐transplantation and the degree of graft‐mediated neurite outgrowth was analyzed.Results:  Embryonic VM manifested a greater capacity for neurite formation and outgrowth on xenogenic tissue, which was shown to be significant using co‐cultures of cortical cells. The transplantation study showed that xenograft‐derived fibres had a greater capacity for extensive fibre projection compared with those originating from allografts.Conclusion:  Results from the present study provide evidence for the hypothesis that xenografts are less responsive to inhibitory molecules present in the adult host environment and as such can project over great distances. Thus neural xenotransplantation may have the potential for more complete circuit reconstruction within the damaged host brain than equivalent allografted tissue.
‘On being both professional and human’: a response
Authors: Little M. 
Published: April 2006

AbstractA recent publication in theInternal Medicine Journaltouches on some sensitive points. It emphasizes deficiencies in communication between doctors and patients and between doctors and families of the patients, particularly in extreme medical circumstances that are likely to end in death. It stresses as well the trauma of seeing a loved one reduced from a human being with a distinctive biography to an impersonal clinical problem. Such articles have a long history but seldom produce any change in the attitudes or practices of the medical profession. There seem to be a number of reasons for this, including clinicians’ ambivalence towards the real importance of ethics in medicine and the lack of a forum in which consumers and doctors might air and discuss their experiences of suffering and disappointment. A forum for mutual discussion is suggested as the most constructive step to take. Medical education has not proven to be an answer to the problems of sensitive communication.
Insulin therapy in type 2 diabetes patients failing oral agents: cost‐effectiveness of biphasic insulin aspart 70/30 vs. insulin glargine in the US*
Authors: Ray J. A. , Valentine W. J. , Roze S. , Nicklasson L. , Cobden D. , Raskin P. , Garber A. , Palmer A. J. 
Published: April 2006

Objectives: To project the long‐term clinical and economic outcomes of treatment with biphasic insulin aspart 30 (BIAsp 70/30, 30% soluble and 70% protaminated insulin aspart) vs. insulin glargine in insulin‐naïve type 2 diabetes patients failing to achieve glycemic control with oral antidiabetic agents alone (OADs).Methods: Baseline patient characteristics and treatment effect data from the recent ‘INITIATE’ clinical trial served as input to a peer‐reviewed, validated Markov/Monte‐Carlo simulation model. INITIATE demonstrated improvements in HbA1c favouring BIAsp 70/30 vs. glargine (−0.43%; p < 0.005) and greater efficacy in reaching glycaemic targets among patients poorly controlled on OAD therapy. Effects on life expectancy (LE), quality‐adjusted life expectancy (QALE), cumulative incidence of diabetes‐related complications and direct medical costs (2004 USD) were projected over 35 years. Clinical outcomes and costs were discounted at a rate of 3.0%per annum. Sensitivity analyses were performed.Results: Improvements in glycaemic control were projected to lead to gains in LE (0.19 ± 0.24 years) and QALE (0.19 ± 0.17 years) favouring BIAsp 70/30 vs. glargine. Treatment with BIAsp 70/30 was also associated with reductions in the cumulative incidences of diabetes‐related complications, notably in renal and retinal conditions. The incremental cost‐effectiveness ratio was $46 533 per quality‐adjusted life year gained with BIAsp 70/30 vs. glargine (for patients with baseline HbA1c ≥ 8.5%, it was $34 916). Total lifetime costs were compared to efficacy rates in both arms as a ratio, which revealed that the lifetime cost per patient treated successfully to target HbA1c levels of <7.0% and ≤ 6.5% were $80 523 and $93 242 lower with BIAsp 70/30 than with glargine, respectively.Conclusions: Long‐term treatment with BIAsp 70/30 was projected to be cost‐effective for patients with type 2 diabetes insufficiently controlled on OADs alone compared to glargine. Treatment with BIAsp 70/30 was estimated to represent an appropriate investment of healthcare dollars in the management of type 2 diabetes.
Causal connections in the acquisition of an orthographic rule: a test of Uta Frith's developmental hypothesis
Authors: Davis Claire , Bryant Peter 
Published: April 2006

Background:  In a longitudinal study we tested Frith's causal hypothesis that children first gain orthographic knowledge through reading and then later, as a consequence, through spelling.Method:  Children from Years 2 and 3 were tested three times over two years on their reading and spelling of pseudo‐words which conformed to the conditional orthographic rule, the ‘final –e’ or ‘split‐digraph’ rule.Results:  Cross‐lagged panel correlation analyses suggested that the children's success in reading split‐digraph words was a causal determinant of their learning to use split‐digraphs in spelling, in the 7‐ to 8‐year period and, with one year‐group but not with the other, in the 8‐ to 9‐year period. In the 9‐ to 10‐year period children's success in reading no longer seemed to affect their spelling.Conclusions:  These results strongly support Frith's causal hypothesis about the development of orthographic knowledge.
Isolation and characterization of polymorphic microsatellite markers for peacock wrasse (Symphodus tinca)
Authors: GALARZA J. A. , CARRERAS‐CARBONELL J. , MACPHERSON E. , TURNER G. F. , RICO C. 
Published: April 2006

AbstractEight polymorphic microsatellite loci were isolated and characterized for the peacock wrasse (Symphodus tinca), a labrid fish inhabiting the Mediterranean and Black seas. Characterization of 35 individuals from the western Mediterranean indicated a relatively high allelic diversity (mean = 12.4, range 9–17), and observed heterozygosity ranging from 0.65 to 0.91. We found no evidence of linkage disequilibrium between pairs of loci. Two loci showed significant departure from Hardy–Weinberg equilibrium. These polymorphic markers can be useful in most basic population genetic applications.
Differential regulation of IL‐2 and IL‐4 in patients with tobacco‐related oral squamous cell carcinoma
Authors: Manchanda P , Sharma SC , Das SN 
Published: April 2006

Aim: The aim of the study was to investigate the systemic immunity in terms of major lymphocyte subsets and the expression of IL‐2 and IL‐4 in T‐cell subsets from peripheral blood of patients with tobacco‐related intraoral squamous cell carcinoma.Methods: CD3+, CD4+and CD8+T‐cell subsets and CD16+ CD56+natural killer cells, and intracellular cytokines in T‐cell subsets were determined by two‐colour flow cytometry and confocal microscopy.Results: Oral cancer patients showed a significantly reduced (P < 0.001) CD3+and CD4+T‐cell subsets with a lower CD4/CD8 ratio when compared with the normal controls. The frequency of CD3+ IL‐4+and CD8+ IL‐4+T cells were significantly higher (P < 0.001) while CD4+ IL‐2+were significantly lower (P < 0.02) in patients when compared with the normal controls. Late stage of the tumour was associated with reduced expression of IL‐2 in both CD4+(P < 0.05) and CD8+(P < 0.03) subsets.Conclusions: The tobacco‐related intraoral squamous cell carcinoma seems to be associated with multiple systemic immune defects particularly, an impaired CD3+and CD4+T cells in the peripheral blood as well as a differential regulation of IL‐2 and IL‐4 in CD4+and CD8+T‐cell subsets. The cytokine response in these patients seems to be skewed from protective Th1 to immunosuppressive Th2 type. Thus these patients could be ideal candidate for immunomodulation therapy.
Prevalence of oral lesions in 13‐ to 16‐year‐old students in Duzce, Turkey
Authors: Parlak AH , Koybasi S , Yavuz T , Yesildal N , Anul H , Aydogan I , Cetinkaya R , Kavak A 
Published: April 2006

Objective:  The aim of this study was to determine the prevalence of oral lesions in 13‐ to 16‐year‐old students.Methods:  A cross‐sectional survey was carried out on students in Duzce, a province in the western Black Sea region of Turkey. A total of 993 children aged between 13 and 16 from eight secondary schools were examined. Oral lesions with recurrent behavior, if observed, were recorded at the time of examination. Venous blood samples were obtained for detecting hemoglobin levels.Results:  Two hundred sixty adolescents (26.2%) were diagnosed with at least one oral mucosal lesion at the time of the examination. Thirteen different mucosal alterations were diagnosed, and the most common lesions were angular cheilitis (9%), linea alba (5.3%), and aphthous ulceration (3.6%). The correlation between occurrence of mucosal lesions and sex was not statistically significant (P > 0.05). Statistical evaluation of the data revealed a significant relationship only between the presence of angular cheilitis and anemia (P < 0.05).Conclusion:  This study is the first epidemiologic study of oral mucosal lesions in adolescents in Turkey. Angular cheilitis was the only oral mucosal lesion that had a significant correlation with anemia.
Blood neutrophil activation markers in severe asthma: lack of inhibition by prednisolone therapy
Authors: Mann Bhupinder S , Chung Kian Fan 
Published: April 2006

Abstract

Background
Neutrophils are increased in the airways and in induced sputum of severe asthma patients. We determined the expression of activation markers from circulating neutrophils in severe asthma, and their supressibility by corticosteroids.

Methods
We compared blood neutrophils from mild, moderate-to-severe and severe steroid-dependent asthma, and non-asthmatics (n = 10 each). We examined the effect of adding or increasing oral prednisolone (30 mg/day;1 week).

Results
Flow cytometric expression of CD35 and CD11b, but not of CD62L or CD18, was increased in severe asthma. F-met-leu-phe increased CD11b, CD35 and CD18 and decreased CD62L expression in all groups, with a greater CD35 increase in severe asthma. In severe steroid-dependent asthma, an increase in prednisolone dose had no effect on neutrophil markers particularly CD62L, but reduced CD11b and CD62L on eosinophils. Phorbol myristate acetate-stimulated oxidative burst and IL-8 release by IL-1β, lipopolysaccharide and GM-CSF in whole blood from mild but not severe asthmatics were inhibited after prednisolone. There were no differences in myeloperoxidase or neutrophil elastase release from purified neutrophils.

Conclusion
Because blood neutrophils in severe asthma are activated and are not inhibited by oral corticosteroids, they may be important in the pathogenesis of severe asthma.
Effect of data normalization on fuzzy clustering of DNA microarray data
Authors: Kim Seo Young , Lee Jae Won , Bae Jong Sung 
Published: April 2006

Abstract

Background
Microarray technology has made it possible to simultaneously measure the expression levels of large numbers of genes in a short time. Gene expression data is information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. Clustering is an important tool for finding groups of genes with similar expression patterns in microarray data analysis. However, hard clustering methods, which assign each gene exactly to one cluster, are poorly suited to the analysis of microarray datasets because in such datasets the clusters of genes frequently overlap.

Results
In this study we applied the fuzzy partitional clustering method known as Fuzzy C-Means (FCM) to overcome the limitations of hard clustering. To identify the effect of data normalization, we used three normalization methods, the two common scale and location transformations and Lowess normalization methods, to normalize three microarray datasets and three simulated datasets. First we determined the optimal parameters for FCM clustering. We found that the optimal fuzzification parameter in the FCM analysis of a microarray dataset depended on the normalization method applied to the dataset during preprocessing. We additionally evaluated the effect of normalization of noisy datasets on the results obtained when hard clustering or FCM clustering was applied to those datasets. The effects of normalization were evaluated using both simulated datasets and microarray datasets. A comparative analysis showed that the clustering results depended on the normalization method used and the noisiness of the data. In particular, the selection of the fuzzification parameter value for the FCM method was sensitive to the normalization method used for datasets with large variations across samples.

Conclusion
Lowess normalization is more robust for clustering of genes from general microarray data than the two common scale and location adjustment methods when samples have varying expression patterns or are noisy. In particular, the FCM method slightly outperformed the hard clustering methods when the expression patterns of genes overlapped and was advantageous in finding co-regulated genes. Thus, the FCM approach offers a convenient method for finding subsets of genes that are strongly associated to a given cluster.
How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results
Authors: Millenaar Frank F , Okyere John , May Sean T , van Zanten Martijn , Voesenek Laurentius ACJ , Peeters Anton JM 
Published: April 2006

Abstract

Background
Short oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operating Software (MAS or GCOS) from Affymetrix. Recently, more methods to analyse the raw data have become available. Ideally all these methods should come up with more or less the same results. We set out to evaluate the different methods and include work on our own data set, in order to test which method gives the most reliable results.

Results
Calculating gene expression with 6 different algorithms (MAS5, dChip PMMM, dChip PM, RMA, GC-RMA and PDNN) using the same (Arabidopsis) data, results in different calculated gene expression levels. Consequently, depending on the method used, different genes will be identified as differentially regulated. Surprisingly, there was only 27 to 36% overlap between the different methods. Furthermore, 47.5% of the genes/probe sets showed good correlation between the mismatch and perfect match intensities.

Conclusion
After comparing six algorithms, RMA gave the most reproducible results and showed the highest correlation coefficients with Real Time RT-PCR data on genes identified as differentially expressed by all methods. However, we were not able to verify, by Real Time RT-PCR, the microarray results for most genes that were solely calculated by RMA. Furthermore, we conclude that subtraction of the mismatch intensity from the perfect match intensity results most likely in a significant underestimation for at least 47.5% of the expression values. Not one algorithm produced significant expression values for genes present in quantities below 1 pmol. If the only purpose of the microarray experiment is to find new candidate genes, and too many genes are found, then mutual exclusion of the genes predicted by contrasting methods can be used to narrow down the list of new candidate genes by 64 to 73%.
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
Authors: Dutheil Julien , Gaillard Sylvain , Bazin Eric , Glémin Sylvain , Ranwez Vincent , Galtier Nicolas , Belkhir Khalid 
Published: April 2006

Abstract

Background
A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/ouput methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications.

Results
We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus.

Conclusion
Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins
Authors: Bagos Pantelis G , Liakopoulos Theodore D , Hamodrakas Stavros J 
Published: April 2006

Abstract

Background
Hidden Markov Models (HMMs) have been extensively used in computational molecular biology, for modelling protein and nucleic acid sequences. In many applications, such as transmembrane protein topology prediction, the incorporation of limited amount of information regarding the topology, arising from biochemical experiments, has been proved a very useful strategy that increased remarkably the performance of even the top-scoring methods. However, no clear and formal explanation of the algorithms that retains the probabilistic interpretation of the models has been presented so far in the literature.

Results
We present here, a simple method that allows incorporation of prior topological information concerning the sequences at hand, while at the same time the HMMs retain their full probabilistic interpretation in terms of conditional probabilities. We present modifications to the standard Forward and Backward algorithms of HMMs and we also show explicitly, how reliable predictions may arise by these modifications, using all the algorithms currently available for decoding HMMs. A similar procedure may be used in the training procedure, aiming at optimizing the labels of the HMM's classes, especially in cases such as transmembrane proteins where the labels of the membrane-spanning segments are inherently misplaced. We present an application of this approach developing a method to predict the transmembrane regions of alpha-helical membrane proteins, trained on crystallographically solved data. We show that this method compares well against already established algorithms presented in the literature, and it is extremely useful in practical applications.

Conclusion
The algorithms presented here, are easily implemented in any kind of a Hidden Markov Model, whereas the prediction method (HMM-TM) is freely available for academic users at http://bioinformatics.biol.uoa.gr/HMM-TM, offering the most advanced decoding options currently available.