bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineralogy of stalactites formed by subaerial weathering of natrocarbonatite hornitos at Oldoinyo Lengai, Tanzania
Authors: Mitchell R. H. 
Published: October 2006

AbstractStalactites formed by the chemical weathering of natrocarbonatite lava decorate the roofs of hollow inactive hornitos at Oldoinyo Lengai, Tanzania. The stalactites are composed principally of trona with lesser and very variable amounts of nahcolite, (NaHCO3), thermonatrite (Na2CO3.H2O), aphthitalite [(K,Na)3Na(SO4)2], kogarkoite [Na3(SO4)F], schairerite [Na21 (SO4)7F6Cl], halite and sylvite. Stalactites are considered to form by the evaporation of Ca-free highly alkaline brines seeping from the altered lavas which form the roofs of the hornitos. The principal subaerial weathering products of natrocarbonatite, i.e. pirsonnite, gaylussite, shortite and calcite are not found in the stalactites and are retained in the altered lavas of the homito roof. Fluorine required for the formation of kogarkoite and schairerite is derived from the decomposition of fluorite at high pH (>10). Sulphur is derived from the decomposition of gregoryite.
SVRMHC prediction server for MHC-binding peptides
Authors: Wan Ji , Liu Wen , Xu Qiqi , Ren Yongliang , Flower Darren R , Li Tongbin 
Published: October 2006

AbstractBackgroundThe binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accuratein silicoprediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort.ResultsRecently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods.ConclusionSVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers.
Goulphar: rapid access and expertise for standard two-color microarray normalization methods
Authors: Lemoine Sophie , Combes Florence , Servant Nicolas , Le Crom Stéphane 
Published: October 2006

Abstract

Background
Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packages but it is often difficult to identify the most appropriate method. Furthermore, the use of R commands for functions and graphics can introduce mistakes that are difficult to trace. We present here a script written in R that provides a flexible means of access to and monitoring of data normalization for two-color microarrays. This script combines the power of BioConductor and R analysis functions and reduces the amount of R programming required.

Results
Goulphar was developed in and runs using the R language and environment. It combines and extends functions found in BioConductor packages (limma and marray) to correct for dye biases and spatial artifacts. Goulphar provides a wide range of optional and customizable filters for excluding incorrect signals during the pre-processing step. It displays informative output plots, enabling the user to monitor the normalization process, and helps adapt the normalization method appropriately to the data. All these analyses and graphical outputs are presented in a single PDF report.

Conclusion
Goulphar provides simple, rapid access to the power of the R/BioConductor statistical analysis packages, with precise control and visualization of the results obtained. Complete documentation, examples and online forms for setting script parameters are available from http://transcriptome.ens.fr/goulphar/.
SNP-PHAGE – High throughput SNP discovery pipeline
Authors: Matukumalli Lakshmi K , Grefenstette John J , Hyten David L , Choi Ik-Young , Cregan Perry B , Van Tassell Curtis P 
Published: October 2006

AbstractBackgroundSingle nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs or microsatellite) markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in a relational database to facilitate interrogation through queries or to generate data for further analyses such as determination of linkage disequilibrium and identification of common haplotypes. Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable.ResultsWe developed SNP-PHAGE (SNPdiscoveryPipeline with additional features for identification of common haplotypes within a sequence tagged site (HaplotypeAnalysis) andGenBank (-dbSNP) submissions. This tool was applied for analyzing sequence traces from diverse soybean genotypes to discover over 10,000 SNPs. This package was developed on UNIX/Linux platform, written in Perl and uses a MySQL database. Scripts to generate a user-friendly web interface are also provided with common queries for preliminary data analysis. A machine learning tool developed by this group for increasing the efficiency of SNP discovery is integrated as a part of this package as an optional feature. The SNP-PHAGE package is being made available open source athttp://bfgl.anri.barc.usda.gov/ML/snp-phage/.ConclusionSNP-PHAGE provides a bioinformatics solution for high throughput SNP discovery, identification of common haplotypes within an amplicon, and GenBank (dbSNP) submissions. SNP selection and visualization are aided through a user-friendly web interface. This tool is useful for analyzing sequence tagged sites (STSs) of genomic sequences, and this software can serve as a starting point for groups interested in developing SNP markers.
Evaluating different methods of microarray data normalization
Authors: Fujita André , Sato João Ricardo , Rodrigues Leonardo de Oliveira , Ferreira Carlos Eduardo , Sogayar Mari Cleide 
Published: October 2006

Abstract

Background
With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration.

Results
Here, we considered three commonly used normalization approaches, namely: Loess, Splines and Wavelets, and two non-parametric regression methods, which have yet to be used for normalization, namely, the Kernel smoothing and Support Vector Regression. The results obtained were compared using artificial microarray data and benchmark studies. The results indicate that the Support Vector Regression is the most robust to outliers and that Kernel is the worst normalization technique, while no practical differences were observed between Loess, Splines and Wavelets.

Conclusion
In face of our results, the Support Vector Regression is favored for microarray normalization due to its superiority when compared to the other methods for its robustness in estimating the normalization curve.
Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs
Authors: López-Giráldez Francesc , Andrés Olga , Domingo-Roura Xavier , Bosch Montserrat 
Published: October 2006

Abstract
Background
The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution.

Results
We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability.

Conclusion
Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.
Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding their use as genetic markers.
Molecular characterization of a DNA fragment harboring the replicon of pBMB165 from Bacillus thuringiensis subsp. tenebrionis
Authors: Huang Junyan , Guo Suxia , Mahillon Jacques , Van der Auwera Géraldine A , Wang Li , Han Dongmei , Yu Ziniu , Sun Ming 
Published: October 2006

Abstract

Background

Bacillus thuringiensis belongs to the Bacillus cereus sensu lato group of Gram-positive and spore-forming bacteria. Most isolates of B. thuringiensis can bear many endogenous plasmids, and the number and size of these plasmids can vary widely among strains or subspecies. As far as we know, the replicon of the plasmid pBMB165 is the first instance of a plasmid replicon being isolated from subsp. tenebrionis and characterized.

Results
A 20 kb DNA fragment containing a plasmid replicon was isolated from B. thuringiensis subsp. tenebrionis YBT-1765 and characterized. By Southern blot analysis, this replicon region was determined to be located on pBMB165, the largest detected plasmid (about 82 kb) of strain YBT-1765. Deletion analysis revealed that a replication initiation protein (Rep165), an origin of replication (ori165) and an iteron region were required for replication. In addition, two overlapping ORFs (orf6 and orf10) were found to be involved in stability control of plasmid. Sequence comparison showed that the replicon of pBMB165 was homologous to the pAMβ1 family replicons, indicating that the pBMB165 replicon belongs to this family. The presence of five transposable elements or remnants thereof in close proximity to and within the replicon control region led us to speculate that genetic exchange and recombination are potentially responsible for the divergence among the replicons of this plasmid family.

Conclusion
The replication and stability features of the pBMB165 from B. thuringiensis subsp. tenebrionis YBT-1765 were identified. Of particular interest is the homology and divergence shared between the pBMB165 replicon and other pAMβ1 family replicons.
Relative risk for cardiovascular atherosclerotic events after smoking cessation: 6–9 years excess risk in individuals with familial hypercholesterolemia
Authors: Kramer Anneke , Jansen Angelique CM , van Aalst-Cohen Emily S , Tanck Michael WT , Kastelein John JP , Zwinderman Aeilko H 
Published: October 2006

Abstract

Background
Smoking history is often di- or trichotomized into for example "never, ever or current smoking". However, smoking must be treated as a time-dependent covariate when lifetime data is available. In particular, individuals do not smoke at birth, there is usually a wide variation with respect to smoking history, and smoking cessation must also be considered.

Methods
Therefore we analyzed smoking as a time-dependent risk factor for cardiovascular atherosclerotic events in a cohort of 2400 individuals with familial hypercholesterolemia who were followed from birth until 2004. Excess risk after smoking-cessation was modelled in a Cox regression model with linear and exponential decaying trends. The model with the highest likelihood value was used to estimate the decay of the excess risk of smoking.

Results
Atherosclerotic events were observed in 779 patients with familial hypercholesterolemia and 1569 individuals had a smoking history. In the model with the highest likelihood value the risk reduction of smoking after cessation follows a linear pattern with time and it appears to take 6 to 9 years before the excess risk is reduced to zero. The risk of atherosclerotic events due to smoking was estimated as 2.1 (95% confidence interval 1.5; 2.9).

Conclusion
It was concluded that excess risk due to smoking declined linearly after cessation in at least six to nine years.
Gaining insight into the Clinical Practice Guideline development processes: qualitative study in a workshop to implement the GRADE proposal in Spain
Authors: Calderón Carlos , Rotaeche Rafael , Etxebarria Arritxu , Marzo Mercé , Rico Rosa , Barandiaran Marta 
Published: October 2006

Abstract
Background
The GRADE method represents a new approach to grading the quality of evidence and strength of recommendations in the preparation of Clinical Practice Guidelines (CPG). In the context of a pilot study to assess the implementability of the system in Spain, we considered it relevant to gain an insight into the significance of the perceptions and attitudes expressed by the actual experts participating in the system try-out.

Methods
Qualitative research with an ethnographic approach, through non-participant observation and focus groups within the context of a consensus workshop in which 19 CPG experts participated to evaluate the GRADE proposal using 12 evidence tables taken from hypertension, asthma and arthritis CPGs. The interventions were recorded, under a guarantee of confidentiality. The transcriptions and field notes were analyzed, based on a sociological discourse analysis model, and the provisional findings were re-sent to participants in order to improve their validity.

Results
1) Certain problems over procedure and terminology hindered the acceptance of this new method as a common reference system for the preparation of CPGs. 2). A greater closeness to clinical practice was accompanied by concerns over value judgments and subjectivity, with a demand for greater explicitness in the consensus process. 3). The type of "evidence" on which the guidelines are based, how and by whom the evidence is prepared, and what the role of the different actors should be, all constitute unresolved concerns in the CPG preparation and implementation processes. 4). The grading process is not neutral: professional background, prior experience and the degree of leadership all condition the participants' input and interactions.

Conclusion
The findings obtained allow the quantitative evaluation to be better interpreted and, in turn, go beyond the particularities of the GRADE method. Adaptation to the complexities of clinical practice, the need for carefully designed multi-disciplinary work and the reflexivity present in the CPG preparation process, all represent lines of debate that are necessary to improve the CPG quality in the Spanish health care sector.
Serum Levels of Specific Glucuronidated Androgen Metabolites Predict BMD and Prostate Volume in Elderly Men
Authors: Vandenput Liesbeth , Labrie Fernand , Mellström Dan , Swanson Charlotte , Knutsson Thomas , Peeker Ralph , Ljunggren Östen , Orwoll Eric , Eriksson Anna L , Damber Jan-Erik , Ohlsson Claes 
Published: October 2006

Abstract
Androgens are important regulators of bone and prostate health in elderly men. The role of serum levels of glucuronidated androgen metabolites as predictors of BMD and prostate volume in men is unclear. We show that specific glucuronidated androgen metabolites predict BMD and prostate volume in elderly men.
Introduction: Androgens are important regulators of bone and prostate health in elderly men. Local synthesis and degradation of androgens are likely to be important parameters of biological action of androgens in androgen-responsive tissues. The aim of this study was to determine the role of serum levels of glucuronidated androgen metabolites as predictors of BMD and prostate volume in elderly men.
Materials and Methods: A subsample of the population-based Swedish part of the MrOS study (n = 631, average age = 75.9 years) was investigated. Bone parameters were measured using DXA. Serum levels of total testosterone (T) and dihydrotestosterone (DHT) were measured by gas chromatography/mass spectroscopy (GC-MS); androstane-3α,17β-diol-3glucuronide (3G) and androstane-3α,17β-diol-17glucuronide (17G) were measured by liquid chromatography/mass spectroscopy. Prostate volume (n = 159) was measured by transrectal ultrasound.
Results: The general pattern is that two of the glucuronidated androgen metabolites, namely 17G and 3G, are stronger positive predictors of BMD than the bioactive androgens (T and DHT). In addition, 17G is a clear positive predictor of prostate volume, explaining 4.5% of the variance in prostate volume, whereas the bioactive androgens do not display any association with prostate volume.
Conclusions: Serum levels of specific glucuronidated androgen metabolites predict BMD and prostate volume in elderly men. Future studies should determine if the glucuronidated androgen metabolites also reflect other biological correlates of androgenic activity, including prostate cancer, and if low levels might be a marker of general androgen deficiency in men.
Poor Preventive Care Achievement and Program Retention Among Low Birth Weight Infant Medicaid Enrollees
Authors: Shulman Shanna 
Published: October 2006

OBJECTIVE. In this study, I examined the relative odds of achievement of preventive care goals during the first year of life and retention of Medicaid coverage at the end of the first year among Medicaid-enrolled low birth weight infants. Association with maternal prenatal health promotion was also considered.
METHODOLOGY. I used a retrospective case-control design. Low birth weight and normal birth weight infants in the Florida Medicaid program (1995–1999) matched on demographic factors were compared on their relative odds of achievement of preventive care goals and Medicaid program retention using multivariate logistic regression (n = 7510). A subsample of infants with linked maternal claims was used to measure the association of maternal health promotion during the prenatal period.
RESULTS. Low birth weight infants had lower relative odds of achieving preventive care goals during the first year and of retaining Medicaid coverage after the first year compared with infants of normal birth weight. However, when maternal health promotion during the prenatal care period was held constant, birth weight was no longer related to achievement of preventive care goals and program retention. Maternal health promotion was positively associated with achievement of preventive goals and program retention for all infants regardless of birth weight.
CONCLUSIONS. Some Medicaid-enrolled low birth weight infants are at risk for poor health supervision and poor continuity of care through failure to retain coverage. The disproportionate odds of poor health promotion among mothers of low birth weight infants explain much of this deficit. States may want to prioritize preventive care supervision and program reenrollment for children of mothers with evidence of low health promotion. This recommendation is particularly important for infants of low birth weight.
A New Reactive Atom Plasma Technology (RAPT) for Precision Machining: the Etching of ULE® Surfaces
Authors: Fanara C. , Shore P. , Nicholls J.R. , Lyford N. , Kelley J. , Carr J. , Sommer P. 
Published: October 2006

AbstractResults on reactive atom plasma etching performed on ULE® (Corning Ultra Low Expansion) glass samples at atmospheric pressure are presented for the first time. A reactive atomic plasma technology (RAPT®), has been developed by RAPT Industries and employed for the finishing of optical surfaces. An atmospheric pressure argon inductively coupled plasma (ICP) excites a reactive gas injected through its centre. The plume of hot neutral excited species reacts at the substrate yielding controlled and repeatable trenches. In the case of ULE a material removal (up to 0.55 mm3/s) is obtained without pre‐heating the samples. Among the factors influencing the results, an increase in gas concentration at the same power does not change the sample temperature, indicating that thermo‐chemical effects do not influence the removal rates. Due to the plasma constructive constrains, increasing the gas concentration is more practical and of wider effect than increasing the power. The benefits of the process are illustrated and the extension of the technology to large optical surfaces discussed.