bluuebunny/crossref_metadata_2025_split huggingface dataset:
REVERSE MATHEMATICS OF MF SPACES
Authors: MUMMERT CARL 
Published: May 2007

This paper gives a formalization of general topology in second-order arithmetic using countably based MF spaces. This formalization is used to study the reverse mathematics of general topology. For each poset P we let MF (P) denote the set of maximal filters on P endowed with the topology generated by {Np | p ∈ P}, where Np = {F ∈ MF (P) | p ∈ F}. We define a countably based MF space to be a space of the form MF (P) for some countable poset P. The class of countably based MF spaces includes all complete separable metric spaces as well as many nonmetrizable spaces. The following reverse mathematics results are obtained. The proposition that every nonempty Gδ subset of a countably based MF space is homeomorphic to a countably based MF space is equivalent to [Formula: see text] over ACA0. The proposition that every uncountable closed subset of a countably based MF space contains a perfect set is equivalent over [Formula: see text] to the proposition that [Formula: see text] is countable for all A ⊆ ℕ. The proposition that every regular countably based MF space is homeomorphic to a complete separable metric space is equivalent to [Formula: see text] over [Formula: see text].
Pivotal contributions of megakaryocytes to the biology of idiopathic myelofibrosis
Authors: Ciurea Stefan O. , Merchant Delwin , Mahmud Nadim , Ishii Takefumi , Zhao Yan , Hu Wenyang , Bruno Edward , Barosi Giovanni , Xu Mingjiang , Hoffman Ronald 
Published: May 2007

AbstractIn order to investigate the biologic processes underlying and resulting from the megakaryocytic hyperplasia that characterizes idiopathic myelofibrosis (IMF), peripheral blood CD34+ cells isolated from patients with IMF, polycythemia vera (PV), and G-CSF–mobilized healthy volunteers were cultured in the presence of stem cell factor and thrombopoietin. IMF CD34+ cells generated 24-fold greater numbers of megakaryocytes (MKs) than normal CD34+ cells. IMF MKs were also shown to have a delayed pattern of apoptosis and to overexpress the antiapoptotic protein bcl-xL. MK hyperplasia in IMF is, therefore, likely a consequence of both the increased ability of IMF progenitor cells to generate MKs and a decreased rate of MK apoptosis. Media conditioned (CM) by CD61+ cells generated in vitro from CD34+ cells were then assayed for the levels of growth factors and proteases. Higher levels of transforming growth factor-β (TGF-β) and active matrix metalloproteinase-9 (MMP9) were observed in media conditioned with IMF CD61+ cells than normal or PV CD61+ cells. Both normal and IMF CD61+ cells produced similar levels of VEGF. MK-derived TGF-B and MMP-9, therefore, likely contribute to the development of many pathological epiphenomena associated with IMF.
Body mass index is associated with reduced exhaled nitric oxide and higher exhaled 8-isoprostanes in asthmatics
Authors: Komakula Sushma , Khatri Sumita , Mermis Joel , Savill Samira , Haque Shireen , Rojas Mauricio , Brown LouAnn , Teague Gerald W , Holguin Fernando 
Published: May 2007

AbstractBackgroundRecently, it has been shown that increasing body mass index (BMI) in asthma is associated with reduced exhaled NO. Our objective in this study was to determine if the BMI-related changes in exhaled NO differ across asthmatics and controls, and to determine if these changes are related to increased airway oxidative stress and systemic levels of leptin and adiponectin.MethodsObservational study of the association of BMI, leptin, and adiponectin with exhaled nitric oxide (NO) and exhaled 8-isoprostanes in 67 non-smoking patients with moderate to severe persistent asthma during baseline conditions and 47 controls. Measurements included plasma levels of leptin, adiponectin, exhaled breath condensates for 8-isoprostanes, exhaled NO, pulmonary function tests, and questionnaires regarding asthma severity and control.ResultsIn asthmatics, BMI and the ratio of leptin to adiponectin were respectively associated with reduced levels of exhaled NO (β = -0.04 [95% C.I. -0.07, -0.1], p < 0.003) and (β = -0.0018 [95% C.I. -0.003, -0.00034], p = 0.01) after adjusting for confounders. Also, BMI was associated with increased levels of exhaled 8-isoprostanes (β = 0.30 [95% C.I. 0.003, 0.6], p = 0.03) after adjusting for confounders. In contrast, we did not observe these associations in the control group of healthy non-asthmatics with a similar weight distribution.ConclusionIn adults with stable moderate to severe persistent asthma, but not in controls, BMI and the plasma ratio of leptin/adiponectin is associated with reduced exhaled NO. Also, BMI is associated with increased exhaled 8-isoprostanes. These results suggest that BMI in asthmatics may increase airway oxidative stress and could explain the BMI-related reductions in exhaled NO.
Greigite: a true intermediate on the polysulfide pathway to pyrite
Authors: Hunger Stefan , Benning Liane G 
Published: May 2007

AbstractThe formation of pyrite (FeS2) from iron monosulfide precursors in anoxic sediments has been suggested to proceed via mackinawite (FeS) and greigite (Fe3S4). Despite decades of research, the mechanisms of pyrite formation are not sufficiently understood because solid and dissolved intermediates are oxygen-sensitive and poorly crystalline and therefore notoriously difficult to characterize and quantify.In this study, hydrothermal synchrotron-based energy dispersive X-ray diffraction (ED-XRD) methods were used to investigate in situ and in real-time the transformation of mackinawite to greigite and pyrite via the polysulfide pathway. The rate of formation and disappearance of specific Bragg peaks during the reaction and the changes in morphology of the solid phases as observed with high resolution microscopy were used to derive kinetic parameters and to determine the mechanisms of the reaction from mackinawite to greigite and pyrite.The results clearly show that greigite is formed as an intermediate on the pathway from mackinawite to pyrite. The kinetics of the transformation of mackinawite to greigite and pyrite follow a zero-order rate law indicating a solid-state mechanism. The morphology of greigite and pyrite crystals formed under hydrothermal conditions supports this conclusion and furthermore implies growth of greigite and pyrite by oriented aggregation of nanoparticulate mackinawite and greigite, respectively. The activation enthalpies and entropies of the transformation of mackinawite to greigite, and of greigite to pyrite were determined from the temperature dependence of the rate constants according to the Eyring equation. Although the activation enthalpies are uncharacteristic of a solid-state mechanism, the activation entropies indicate a large increase of order in the transition state, commensurate with a solid-state mechanism.
Magnetic record associated with tree ring density: Possible climate proxy
Authors: Kletetschka Gunther , Pruner Petr , Venhodova Daniela , Kadlec Jaroslav 
Published: May 2007

AbstractA magnetic signature of tree rings was tested as a potential paleo-climatic indicator. We examined wood from sequoia tree, located in Mountain Home State Forest, California, whose tree ring record spans over the period 600 – 1700 A.D. We measured low and high-field magnetic susceptibility, the natural remanent magnetization (NRM), saturation isothermal remanent magnetization (SIRM), and stability against thermal and alternating field (AF) demagnetization. Magnetic investigation of the 200 mm long sequoia material suggests that magnetic efficiency of natural remanence may be a sensitive paleoclimate indicator because it is substantially higher (in average >1%) during the Medieval Warm Epoch (700–1300 A.D.) than during the Little Ice Age (1300–1850 A.D.) where it is <1%. Diamagnetic behavior has been noted to be prevalent in regions with higher tree ring density. The mineralogical nature of the remanence carrier was not directly detected but maghemite is suggested due to low coercivity and absence of Verwey transition. Tree ring density, along with the wood's magnetic remanence efficiency, records the Little Ice Age (LIA) well documented in Europe. Such a record suggests that the European LIA was a global phenomenon. Magnetic analysis of the thermal stability reveals the blocking temperatures near 200 degree C. This phenomenon suggests that the remanent component in this tree may be thermal in origin and was controlled by local thermal condition.
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise
Authors: Mantini Dante , Petrucci Francesca , Pieragostino Damiana , Del Boccio Piero , Di Nicola Marta , Di Ilio Carmine , Federici Giorgio , Sacchetta Paolo , Comani Silvia , Urbani Andrea 
Published: May 2007

Abstract

Background
Mass spectrometry protein profiling is a promising tool for biomarker discovery in clinical proteomics. However, the development of a reliable approach for the separation of protein signals from noise is required. In this paper, LIMPIC, a computational method for the detection of protein peaks from linear-mode MALDI-TOF data is proposed. LIMPIC is based on novel techniques for background noise reduction and baseline removal. Peak detection is performed considering the presence of a non-homogeneous noise level in the mass spectrum. A comparison of the peaks collected from multiple spectra is used to classify them on the basis of a detection rate parameter, and hence to separate the protein signals from other disturbances.

Results
LIMPIC preprocessing proves to be superior than other classical preprocessing techniques, allowing for a reliable decomposition of the background noise and the baseline drift from the MALDI-TOF mass spectra. It provides lower coefficient of variation associated with the peak intensity, improving the reliability of the information that can be extracted from single spectra. Our results show that LIMPIC peak-picking is effective even in low protein concentration regimes. The analytical comparison with commercial and freeware peak-picking algorithms demonstrates its superior performances in terms of sensitivity and specificity, both on in-vitro purified protein samples and human plasma samples.

Conclusion
The quantitative information on the peak intensity extracted with LIMPIC could be used for the recognition of significant protein profiles by means of advanced statistic tools: LIMPIC might be valuable in the perspective of biomarker discovery.
Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes
Authors: Rasmussen John P , Saint Christopher P , Monis Paul T 
Published: May 2007

Abstract

Background
DNA melting curve analysis using double-stranded DNA-specific dyes such as SYTO9 produce complex and reproducible melting profiles, resulting in the detection of multiple melting peaks from a single amplicon and allowing the discrimination of different species. We compare the melting curves of several Naegleria and Cryptosporidium amplicons generated in vitro with in silico DNA melting simulations using the programs POLAND and MELTSIM., then test the utility of these programs for assay design using a genetic marker for toxin production in cyanobacteria.

Results
The SYTO9 melting curve profiles of three species of Naegleria and two species of Cryptosporidium were similar to POLAND and MELTSIM melting simulations, excepting some differences in the relative peak heights and the absolute melting temperatures of these peaks. MELTSIM and POLAND were used to screen sequences from a putative toxin gene in two different species of cyanobacteria and identify regions exhibiting diagnostic melting profiles. For one of these diagnostic regions the POLAND and MELTSIM melting simulations were observed to be different, with POLAND more accurately predicting the melting curve generated in vitro. Upon further investigation of this region with MELTSIM, inconsistencies between the melting simulation for forward and reverse complement sequences were observed. The assay was used to accurately type twenty seven cyanobacterial DNA extracts in vitro.

Conclusion
Whilst neither POLAND nor MELTSIM simulation programs were capable of exactly predicting DNA dissociation in the presence of an intercalating dye, the programs were successfully used as tools to identify regions where melting curve differences could be exploited for diagnostic melting curve assay design. Refinements in the simulation parameters would be required to account for the effect of the intercalating dye and salt concentrations used in real-time PCR. The agreement between the melting curve simulations for different species of Naegleria and Cryptosporidium and the complex melting profiles generated in vitro using SYTO9 verified that the complex melting profile of PCR amplicons was solely the result of DNA dissociation. Other data outputs from these simulations were also used to identify the melting domains that contributed to the observed melting peaks for each of the different PCR amplicons.
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
Authors: Lu Jun , Lee Joseph C , Salit Marc L , Cam Margaret C 
Published: May 2007

Abstract

Background
Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis.

Results
Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance.

Conclusion
We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software.
Colony size measurement of the yeast gene deletion strains for functional genomics
Authors: Memarian Negar , Jessulat Matthew , Alirezaie Javad , Mir-Rashed Nadereh , Xu Jianhua , Zareie Mehri , Smith Myron , Golshani Ashkan 
Published: May 2007

Abstract

Background
Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences.

Results
Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research.

Conclusion
GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.
UbiProt: a database of ubiquitylated proteins
Authors: Chernorudskiy Alexander L , Garcia Alejandro , Eremin Eugene V , Shorina Anastasia S , Kondratieva Ekaterina V , Gainullin Murat R 
Published: May 2007

Abstract

Background
Post-translational protein modification with ubiquitin, or ubiquitylation, is one of the hottest topics in a modern biology due to a dramatic impact on diverse metabolic pathways and involvement in pathogenesis of severe human diseases. A great number of eukaryotic proteins was found to be ubiquitylated. However, data about particular ubiquitylated proteins are rather disembodied.

Description
To fill a general need for collecting and systematizing experimental data concerning ubiquitylation we have developed a new resource, UbiProt Database, a knowledgebase of ubiquitylated proteins. The database contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and de-ubiquitylation machinery and literature references reflecting experimental evidence of ubiquitylation. UbiProt is available at http://ubiprot.org.ru for free.

Conclusion
UbiProt Database is a public resource offering comprehensive information on ubiquitylated proteins. The resource can serve as a general reference source both for researchers in ubiquitin field and those who deal with particular ubiquitylated proteins which are of their interest. Further development of the UbiProt Database is expected to be of common interest for research groups involved in studies of the ubiquitin system.
Discarding duplicate ditags in LongSAGE analysis may introduce significant error
Authors: Emmersen Jeppe , Heidenblut Anna M , Høgh Annabeth Laursen , Hahn Stephan A , Welinder Karen G , Nielsen Kåre L 
Published: May 2007

AbstractBackgroundDuring gene expression analysis by Serial Analysis of Gene Expression (SAGE), duplicate ditags are routinely removed from the data analysis, because they are suspected to stem from artifacts during SAGE library construction. As a consequence, naturally occurring duplicate ditags are also removed from the analysis leading to an error of measurement.ResultsAn algorithm was developed to analyze the differential occurrence of SAGE tags in different ditag combinations. Analysis of a pancreatic acinar cell LongSAGE library showed no sign of a general amplification bias that justified the removal of all duplicate ditags. Extending the analysis to 10 additional LongSAGE libraries showed no justification for removal of all duplicate ditags either. On the contrary, while the error introduced in original SAGE by removal of naturally occurring duplicate ditags is insignificant, it leads to an error of up to 3 fold in LongSAGE. However, the algorithm developed for the analysis of duplicate ditags was able to identify individual artifact ditags that originated from rare nucleotide variations of tags and vector contamination.ConclusionThe removal of all duplicate ditags was unfounded for the datasets analyzed and led to large errors. This may also be the case for other LongSAGE datasets already present in databases. Analysis of the ditag population, however, can identify artifact tags that should be removed from analysis or have their tag count adjusted.
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
Authors: Zhu Huaiqiu , Hu Gang-Qing , Yang Yi-Fan , Wang Jin , She Zhen-Su 
Published: May 2007

Abstract

Background
Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes.

Results
This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs) and Translation Initiation Sites (TISs). The former is based on a linguistic "Entropy Density Profile" (EDP) model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED) algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes.

Conclusion
Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.
In silico segmentations of lentivirus envelope sequences
Authors: Boissin-Quillon Aurélia , Piau Didier , Leroux Caroline 
Published: May 2007

Abstract

Background
The gene encoding the envelope of lentiviruses exhibits a considerable plasticity, particularly the region which encodes the surface (SU) glycoprotein. Interestingly, mutations do not appear uniformly along the sequence of SU, but they are clustered in restricted areas, called variable (V) regions, which are interspersed with relatively more stable regions, called constant (C) regions. We look for specific signatures of C/V regions, using hidden Markov models constructed with SU sequences of the equine, human, small ruminant and simian lentiviruses.

Results
Our models yield clear and accurate delimitations of the C/V regions, when the test set and the training set were made up of sequences of the same lentivirus, but also when they were made up of sequences of different lentiviruses. Interestingly, the models predicted the different regions of lentiviruses such as the bovine and feline lentiviruses, not used in the training set. Models based on composite training sets produce accurate segmentations of sequences of all these lentiviruses.

Conclusion
Our results suggest that each C/V region has a specific statistical oligonucleotide composition, and that the C (respectively V) regions of one of these lentiviruses are statistically more similar to the C (respectively V) regions of the other lentiviruses, than to the V (respectively C) regions of the same lentivirus.