bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing disability progression with the Multiple Sclerosis Functional Composite
Authors: Rudick RA , Polman CH , Cohen JA , Walton MK , Miller AE , Confavreux C , Lublin FD , Hutchinson M , O’Connor PW , Schwid SR , Balcer LJ , Lynn F , Panzara MA , Sandrock AW 
Published: August 2009

Background The initial Multiple Sclerosis Functional Composite (MSFC) proposal was a three-part composite of quantitative measures of ambulation, upper extremity function, and cognitive function expressed as a single composite Z-score. However, the clinical meaning of an MSFC Z-score change is not obvious. This study instead used MSFC component data to define a patient-specific disease progression event. Objective Evaluate a new method for analyzing disability progression using the MSFC. Methods MSFC progression was defined as worsening from baseline on scores of at least one MSFC component by 20% (MSFC Progression-20) or 15% (MSFC Progression-15), sustained for ≥3 months. Progression rates were determined using data from natalizumab clinical studies (Natalizumab Safety and Efficacy in Relapsing Remitting Multiple Sclerosis [AFFIRM] and Safety and Efficacy of Natalizumab in Combination With Interferon Beta-1a in Patients With Relapsing Remitting Multiple Sclerosis [SENTINEL]). Correlations between MSFC progression and other clinical measures were determined, as was sensitivity to treatment effects. Results Substantial numbers of patients met MSFC progression criteria, with MSFC Progression-15 being more sensitive than MSFC Progression-20, at both 1 and 2 years. MSFC Progression-20 and MSFC Progression-15 were related significantly to Expanded Disability Status Scale (EDSS) score change, relapse rate, and the SF-36 Physical Component Summary (PCS) score change. MSFC Progression-20 and MSFC Progression-15 at 1 year were predictive of EDSS progression at 2 years. Both MSFC progression end points demonstrated treatment effects in AFFIRM, and results were replicated in SENTINEL. Conclusion MSFC Progression-20 and MSFC Progression-15 are sensitive measures of disability progression; correlate with EDSS, relapse rates, and SF-36 PCS; and are capable of demonstrating therapeutic effects in randomized, controlled clinical studies.
Course of neuromyelitis optica during inadvertent pregnancy in a patient treated with rituximab
Authors: Pellkofer HL , Suessmair C , Schulze A , Hohlfeld R , Kuempfel T 
Published: August 2009

In neuromyelitis optica (NMO), the monoclonal B-cell antibody rituximab is a therapeutic option. Little is known about the course of NMO and the safety of rituximab during pregnancy. In this study, we report the clinical course of a patient with NMO after application of rituximab 1 week before inadvertent conception. Mother and child did not experience any adverse event, and the postpartum development of the baby was completely normal up to 15 months. Clinical course of NMO was stable during the entire pregnancy. This case illustrates a favorable outcome in a pregnant NMO patient and her child after therapy with rituximab.
Diffusion in diamond. II. High-pressure-temperature experiments
Authors: Harte B. , Taniguchi T. , Chakraborty S. 
Published: August 2009

AbstractHigh-pressure-temperature (P-T) experiments were conducted in an attempt to determine the diffusion rates of C atoms in diamond, and the possibility of changes in the isotope compositions of diamond at high P-T in the Earth’s mantle. The starting material consisted of a polished plate of natural diamond (very largely 12C), which had been coated with 13C diamond by chemical-vapourdeposition to form a sharp interface between 12C and 13C diamond. Three experiments were performed at 1800, 2000 and 2300ºC, all at 7.7 GPa, for0.5 –20 h. Isotopic profiles obtained by ion microprobe before and after each experiment showed no evidence of relaxation of the sharp interface between 12C and 13C, and so diffusion must have been on a scale less than the ~32 nm depth resolution for this technique. Using 32 nm as the maximum length scale of diffusion across the interface, the maximum ln D (diffusion coefficient) values for the experiments were calculated to be in the range –38 to –42. Unlike previous experimental data, these results show that changes in the isotopic compositions of diamond on long time scales in the Earth’s upper mantle are unlikely. Furthermore, the results support empirical evidence from mapping of C isotope distributions in natural diamonds that C isotope compositions reflect diamond growth compositions.
The geochemistry of Middle Jurassic dykes associated with the Straumsvola–Tvora alkaline plutons, Dronning Maud Land, Antarctica and their association with the Karoo large igneous province
Authors: Riley T. R. , Curtis M. L. , Leat P. T. , Millar I. L. 
Published: August 2009

AbstractJurassic dykes of western Dronning Maud Land (Antarctica) form a minor component of the Karoo large igneous province. An extensive local dyke swarm intrudes Neoproterozoic gneisses and Jurassic syenite plutons on the margins of the Jutulstraumen palaeo rift in the Svedrupfjella region. The dykes were intruded in three distinct episodes (~204, ~176 and ~170 Ma). The 204 Ma dykes are overwhelminglylow-Ti, olivine tholeiites including some primitive (picritic) compositions (MgO >12 wt.%; Fe2O3 >12 wt.%; Cr >1000 ppm; Ni >600 ppm). This 204 Ma event precedes the main Karoo volcanic event by~25 Ma, so anycorrelations to the wider province are difficult to make. However, it mayrecord the earliest phase of rift activity along the Jutulstraumen. The 176 Ma dyke event is more intimately associated with the two syenite plutons. The dykes are alkaline (basanite/ tephrite) and were small-degree melts from an enriched, locallyderived source and underwent at least some degree of interaction with a syenitic contaminant. This ~176 Ma dyke event is widespread elsewhere in the Karoo (southern Africa and Dronning Maud Land). Later-stage (170 Ma) felsic (phonolite–comendite) dykes intrude the 176 Ma basanite–tephrite suite and represent the last phase of magmatic activityin the region.
The crystal structure of tedhadleyite, Hg2+Hg101+O4l2(Cl,Br)2, from the Clear Creek Claim, San Benito County, California
Authors: Cooper M. A. , Hawthorne F. C. 
Published: August 2009

AbstractThe crystal structure of tedhadleyite, ideally Hg2+Hg101+O4l2(Cl,Br)2,triclinic, AĪ, a 7.0147(5), b 11.8508(7), c 12.5985(8) Å, α 115.583(5), β 82.575(2), γ 100.619(2)º, V 927.0(2) Å3, Z = 2,was solved by direct methods and refined to an R1 index of 4.5% for 2677 unique reflections. There are six symmetrically distinct Hg sites in tedhadleyite: Hg(1) is occupied by Hg2+ and Hg(2–6) are occupied by Hg+ that forms three [Hg–Hg]2+ dimers with Hg–Hg separations between 2.527 and 2.556 Å. These [Hg–Hg]2+ dimers have strong covalent bonds to O atoms,forming pseudo-linear O–Hg–Hg–O arrangements,and weak bonds to halogen and O atoms at high angles to the dimer axis. The [O–Hg–Hg-O] groups share anions to form four-membered square rings of composition [Hg8O4] that link along [100] via [O–Hg–Hg-O] groups and along [001] via [O–Hg–O] groups, forming rectangular rings of composition [Hg14O8]. The rings form a corrugated layer that interweaves with a symmetrically related layer whereby the [O–Hg(6)–Hg(6)–O] linking groups of one layer pass through the centres of the square [Hg8O4] rings of the other layer to form [Hg11O4] complex slabs parallel to (010) that link through Hg-I and Hg-Br,Cl bonds.
The crystal structure of Ba2F2(S6+O3S2–), a natural thiosulphate weathering product of old smelting slags at the Surrender Mill, Yorkshire, UK
Authors: Kampf A. R. 
Published: August 2009

AbstractThe crystal structure of Ba2F2(S6+O3S2–), a natural thiosulphate weathering product of old smelting slags at the Surrender Mill, Yorkshire, England, UK, has been solved to R1 = 0.88% for 399 unique [Fo > 4α F] reflections and 0.91% for all 407 reflections. The compound is monoclinic, C2/m, a 15.3172(5), b 4.5898(1), c 4.6320(2) Å, β 101.449(1)º, V 319.17(2) Å3. The structure of Ba2F2(S6+O3S2–) consists of BaF2Ba layer fragments of the fluorite-type structure of frankdicksonite (BaF2) parallel to (100) alternating with layers of thiosulphate groups. The layer sequence in one unit cell is (S6+O3S2–)-BaF2Ba-(S6+O3S2–)-BaF2Ba. The structure resembles that of grandreefite, Pb2F2SO4.
HIV-1 Tat and heparan sulfate proteoglycan interaction: a novel mechanism of lymphocyte adhesion and migration across the endothelium
Authors: Urbinati Chiara , Nicoli Stefania , Giacca Mauro , David Guido , Fiorentini Simona , Caruso Arnaldo , Alfano Massimo , Cassetta Luca , Presta Marco , Rusnati Marco 
Published: August 2009

AbstractThe HIV-1 transactivating factor Tat accumulates on the surface of endothelium by interacting with heparan sulfate proteoglycans (HSPGs). Tat also interacts with B-lymphoid Namalwa cells but only when these overexpress HSPGs after syndecan-1 cDNA transfection (SYN-NCs). Accordingly, SYN-NCs, but not mock-transfected cells, adhere to endothelial cells (ECs) when Tat is bound to the surface of either one of the 2 cell types or when SYN-NCs are transfected with a Tat cDNA. Moreover, endogenously produced Tat bound to cell-surface HSPGs mediates cell adhesion of HIV+ ACH-2 lymphocytes to the endothelium. This heterotypic lymphocyte-EC interaction is prevented by HSPG antagonist or heparinase treatment, but not by integrin antagonists and requires the homodimerization of Tat protein. Tat tethered to the surface of SYN-NCs or of peripheral blood monocytes from healthy donors promotes their transendothelial migration in vitro in response to CXCL12 or CCL5, respectively, and SYN-NC extravasation in vivo in a zebrafish embryo model of inflammation. In conclusion, Tat homodimers bind simultaneously to HSPGs expressed on lymphoid and EC surfaces, leading to HSPG/Tat-Tat/HSPG quaternary complexes that physically link HSPG-bearing lymphoid cells to the endothelium, promoting their extravasation. These data provide new insights about how lymphoid cells extravasate during HIV infection.
R/BHC: fast Bayesian hierarchical clustering for microarray data
Authors: Savage Richard S , Heller Katherine , Xu Yang , Ghahramani Zoubin , Truman William M , Grant Murray , Denby Katherine J , Wild David L 
Published: August 2009

Abstract

Background
Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained.

Results
We present an R/Bioconductor port of a fast novel algorithm for Bayesian agglomerative hierarchical clustering and demonstrate its use in clustering gene expression microarray data. The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge.

Conclusion
Biologically plausible results are presented from a well studied data set: expression profiles of A. thaliana subjected to a variety of biotic and abiotic stresses. Our method avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric.
Correlations between RNA and protein expression profiles in 23 human cell lines
Authors: Gry Marcus , Rimini Rebecca , Strömberg Sara , Asplund Anna , Pontén Fredrik , Uhlén Mathias , Nilsson Peter 
Published: August 2009

Abstract

Background
The Central Dogma of biology holds, in famously simplified terms, that DNA makes RNA makes proteins, but there is considerable uncertainty regarding the general, genome-wide correlation between levels of RNA and corresponding proteins. Therefore, to assess degrees of this correlation we compared the RNA profiles (determined using both cDNA- and oligo-based microarrays) and protein profiles (determined immunohistochemically in tissue microarrays) of 1066 gene products in 23 human cell lines.

Results
A high mean correlation coefficient (0.52) was obtained from the pairwise comparison of RNA levels determined by the two platforms. Significant correlations, with correlation coefficients exceeding 0.445, between protein and RNA levels were also obtained for a third of the specific gene products. However, the correlation coefficients between levels of RNA and protein products of specific genes varied widely, and the mean correlations between the protein and corresponding RNA levels determined using the cDNA- and oligo-based microarrays were 0.25 and 0.20, respectively.

Conclusion
Significant correlations were found in one third of the examined RNA species and corresponding proteins. These results suggest that RNA profiling might provide indirect support to antibodies' specificity, since whenever a evident correlation between the RNA and protein profiles exists, this can sustain that the antibodies used in the immunoassay recognized their cognate antigens.
Multiple displacement amplification for complex mixtures of DNA fragments
Authors: Shoaib Muhammad , Baconnais Sonia , Mechold Undine , Le Cam Eric , Lipinski Marc , Ogryzko Vasily 
Published: August 2009

AbstractBackgroundA fundamental requirement for genomic studies is the availability of genetic material of good quality and quantity. The desired quantity and quality are often hard to obtain when target DNA is composed of complex mixtures of relatively short DNA fragments. Here, we sought to develop a method to representatively amplify such complex mixtures by converting them to long linear and circular concatamers, from minute amounts of starting material, followed by phi29-based multiple displacement amplification.ResultsWe report here proportional amplification of DNA fragments that were first converted into concatamers starting from DNA amounts as low as 1 pg. Religations at low concentration (< 1 ng/μL) preferentially lead to fragment self-circularization, which are then amplified independently, and result in non-uniform amplification. To circumvent this problem, an additional (stuffer) DNA was added during religation (religation concentration > 10 ng/μL), which helped in the formation of long concatamers and hence resulted in uniform amplification. To confirm its usefulness in research, DP1 bound chromatin was isolated through ChIP and presence of DHFR promoter was detected using q-PCR and compared with an irrelevant GAPDH promoter. The results clearly indicated that when ChIP material was religated in presence of stuffer DNA (improved MDA), it allowed to recover the original pattern, while standard MDA and MDA without stuffer DNA failed to do so.ConclusionWe believe that this method allows for generation of abundant amounts of good quality genetic material from a complex mixture of short DNA fragments, which can be further used in high throughput genetic analysis.
Annotation of mammalian primary microRNAs
Authors: Saini Harpreet K , Enright Anton J , Griffiths-Jones Sam 
Published: August 2009

Abstract

Background
MicroRNAs (miRNAs) are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approximately 50% of mammalian miRNAs are expressed from introns of protein-coding genes; the primary transcript (pri-miRNA) is therefore assumed to be the host transcript. However, very little is known about the structure of pri-miRNAs expressed from intergenic regions. Here we annotate transcript boundaries of miRNAs in human, mouse and rat genomes using various transcription features. The 5' end of the pri-miRNA is predicted from transcription start sites, CpG islands and 5' CAGE tags mapped in the upstream flanking region surrounding the precursor miRNA (pre-miRNA). The 3' end of the pri-miRNA is predicted based on the mapping of polyA signals, and supported by cDNA/EST and ditags data. The predicted pri-miRNAs are also analyzed for promoter and insulator-associated regulatory regions.

Results
We define sets of conserved and non-conserved human, mouse and rat pre-miRNAs using bidirectional BLAST and synteny analysis. Transcription features in their flanking regions are used to demarcate the 5' and 3' boundaries of the pri-miRNAs. The lengths and boundaries of primary transcripts are highly conserved between orthologous miRNAs. A significant fraction of pri-miRNAs have lengths between 1 and 10 kb, with very few introns. We annotate a total of 59 pri-miRNA structures, which include 82 pre-miRNAs. 36 pri-miRNAs are conserved in all 3 species. In total, 18 of the confidently annotated transcripts express more than one pre-miRNA. The upstream regions of 54% of the predicted pri-miRNAs are found to be associated with promoter and insulator regulatory sequences.

Conclusion
Little is known about the primary transcripts of intergenic miRNAs. Using comparative data, we are able to identify the boundaries of a significant proportion of human, mouse and rat pri-miRNAs. We confidently predict the transcripts including a total of 77, 58 and 47 human, mouse and rat pre-miRNAs respectively. Our computational annotations provide a basis for subsequent experimental validation of predicted pri-miRNAs.
Genetic characterization of clinical and agri-food isolates of multi drug resistant Salmonella enterica serovar Heidelberg from Canada
Authors: Andrysiak Ashleigh K , Olson Adam B , Tracz Dobryan M , Dore Kathryn , Irwin Rebecca , Ng Lai-King , Gilmour Matthew W ,   Canadian Integrated Program for Antimicrobial Resistance Surveillance Collaborative
Published: August 2009

Abstract

Background

Salmonella enterica serovar Heidelberg ranks amongst the most prevalent causes of human salmonellosis in Canada and an increase in resistance to extended spectrum cephalosporins (ESC) has been observed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance. This study examined the genetic relationship between S. Heidelberg isolates from livestock, abattoir, retail meat, and clinical human specimens to determine whether there was a link between the emergence of MDR S. Heidelberg in chicken agri-food sources and the simultaneous increase of MDR S. Heidelberg in human clinical samples.

Results
Chromosomal genetic homogeneity was observed by pulsed-field gel electrophoresis (PFGE), DNA sequence-based typing (SBT) and DNA microarray-based comparative genomic hybridization (CGH). Sixty one percent of isolates were indistinguishable by PFGE conducted using Xba I and Bln I restriction enzymes. An additional 15% of isolates had PFGE patterns that were closely related to the main cluster. SBT did not identify DNA polymorphisms and CGH revealed only genetic differences between the reference S. Typhimurium strain and S. Heidelberg isolates. Genetic variation observed by CGH between S. Heidelberg isolates could be attributed to experimental variation. Alternatively, plasmid content was responsible for differences in antimicrobial susceptibility, and restriction fragment length polymorphism (RFLP) analyses followed by replicon typing identified two divergent plasmid types responsible for ESC resistance.

Conclusion
Due to the overall limited genetic diversity among the isolates, it was not possible to identify variable traits that would be suitable for source tracking between human and agri-food isolates of S. Heidelberg in Canada.
Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis
Authors: Xia Qiangwei , Wang Tiansong , Hendrickson Erik L , Lie Thomas J , Hackett Murray , Leigh John A 
Published: August 2009

Abstract

Background
Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H2 and other substrates to produce methane. Methanococcus maripaludis is a model for studies of the global response to nutrient limitations.

Results
We used high-coverage quantitative proteomics to determine the response of M. maripaludis to growth-limiting levels of H2, nitrogen, and phosphate. Six to ten percent of the proteome changed significantly with each nutrient limitation. H2 limitation increased the abundance of a wide variety of proteins involved in methanogenesis. However, one protein involved in methanogenesis decreased: a low-affinity [Fe] hydrogenase, which may dominate over a higher-affinity mechanism when H2 is abundant. Nitrogen limitation increased known nitrogen assimilation proteins. In addition, the increased abundance of molybdate transport proteins suggested they function for nitrogen fixation. An apparent regulon governed by the euryarchaeal nitrogen regulator NrpR is discussed. Phosphate limitation increased the abundance of three different sets of proteins, suggesting that all three function in phosphate transport.

Conclusion
The global proteomic response of M. maripaludis to each nutrient limitation suggests a wider response than previously appreciated. The results give new insight into the function of several proteins, as well as providing information that should contribute to the formulation of a regulatory network model.
Virus variation resources at the National Center for Biotechnology Information: dengue virus
Authors: Resch Wolfgang , Zaslavsky Leonid , Kiryutin Boris , Rozanov Michael , Bao Yiming , Tatusova Tatiana A 
Published: August 2009

Abstract

Background
There is an increasing number of complete and incomplete virus genome sequences available in public databases. This large body of sequence data harbors information about epidemiology, phylogeny, and virulence. Several specialized databases, such as the NCBI Influenza Virus Resource or the Los Alamos HIV database, offer sophisticated query interfaces along with integrated exploratory data analysis tools for individual virus species to facilitate extracting this information. Thus far, there has not been a comprehensive database for dengue virus, a significant public health threat.

Results
We have created an integrated web resource for dengue virus. The technology developed for the NCBI Influenza Virus Resource has been extended to process non-segmented dengue virus genomes. In order to allow efficient processing of the dengue genome, which is large in comparison with individual influenza segments, we developed an offline pre-alignment procedure which generates a multiple sequence alignment of all dengue sequences. The pre-calculated alignment is then used to rapidly create alignments of sequence subsets in response to user queries. This improvement in technology will also facilitate the incorporation of additional virus species in the future. The set of virus-specific databases at NCBI, which will be referred to as Virus Variation Resources (VVR), allow users to build complex queries against virus-specific databases and then apply exploratory data analysis tools to the results. The metadata is automatically collected where possible, and extended with data extracted from the literature.

Conclusion
The NCBI Dengue Virus Resource integrates dengue sequence information with relevant metadata (sample collection time and location, disease severity, serotype, sequenced genome region) and facilitates retrieval and preliminary analysis of dengue sequences using integrated web analysis and visualization tools.