bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffusion in diamond. I. Carbon isotope mapping of natural diamond
Authors: Craven J. A. , Harte B. , Fisher D. , Schulze D. J. 
Published: August 2009

AbstractRecent advances in ion microprobe instrumentation and techniques have enabled the mapping of C isotope ratios across the whole of a polished plate of a natural diamond from Guaniamo, Venezuela. The resultant map of C isotope variation closely matches the cathodoluminescence image of the growth structure of the diamond and, therefore, indicates an extremely limited scale of diffusion of C atoms sincethetimeof diamond formation. This result is compatible with thelimite d mobility of N atoms shown by theIaAB aggregation stateof thediamond. Inclusions in thediamond aree clogitic, in common with many Guaniamo diamonds with temperatures of formation of around 1200ºC. At such temperature the IaAB aggregation state indicates a mantle residence time on the order of 1 Ga. Such temperatures of formation and mantle residence times are common to many natural diamonds; thus the extremely limited diffusion of C isotopes shown by the mapping indicates that many diamonds will retain the C isotope compositions of their initial formation.
The Palaeogene Eskdalemuir dyke, Scotland: long-distance lateral transport of rhyolitic magma in a mixed-magma intrusion
Authors: Macdonald R. , Bagiński B. , Upton B. G. J. , Dzierżanowski P. , Marshall-Roberts W. , Prieto M. 
Published: August 2009

AbstractThe Palaeogene Eskdalemuir dyke, part of the Mull dyke swarm in the Southern Uplands of Scotland, is ~60 km long and up to 40 m thick. Its southern tip is 230 km from the inferred source on Mull. The dyke is composite, with tholeiitic basaltic margins and a vitreous central facies ranging from basaltic andesite to andesite in composition. Plagioclase and pyroxene phenocrysts and matrix crystals in the central facies show unusually large compositional ranges and complex textural relationships. Wholerock major and trace-element abundances show linear variations against MgO content, consistent with the rocks in the central facies having formed by mixing of basalt and rhyolite magmas. The rhyolite can be closely matched by rocks from the Mull centre. The mafic and silicic magmas were intruded from a compositionally zoned chamber beneath Mull, perhaps during collapse of the Centre 1 caldera. The lower-viscosity basaltic magma was emplaced before, but lubricated the lateral propagation of, the silicic magma, which mixed with the partially solidified basalt, the proportion of rhyolite increasing towards the dyke centre. The Eskdalemuir dyke represents an unusual, perhaps unique, example of a rhyolite magma being emplaced >200 km from its inferred source. The supposed correlative of the Eskdalemuir dyke north of the Southern Uplands Fault, the Dalraith-Linburn dyke, is not comagmatic with it.
Outcome of congenital acute lymphoblastic leukemia treated on the Interfant-99 protocol
Authors: van der Linden Marieke H. , Valsecchi Maria Grazia , De Lorenzo Paola , Möricke Anja , Janka Gritta , Leblanc Thierry M. , Felice Maria , Biondi Andrea , Campbell Myriam , Hann Ian , Rubnitz Jeffrey E. , Stary Jan , Szczepanski Tomasz , Vora Ajay , Ferster Alina , Hovi Liisa , Silverman Lewis B. , Pieters Rob 
Published: August 2009

AbstractAcute lymphoblastic leukemia (ALL) diagnosed in the first month of life (congenital ALL) is very rare. Although congenital ALL is often assumed to be fatal, no studies have been published on outcome except for case reports. The present study reports the outcome of 30 patients with congenital ALL treated with the uniform Interfant-99 protocol, a hybrid regimen combining ALL treatment with elements designed for treatment of acute myeloid leukemia. Congenital ALL was characterized by a higher white blood cell count and a strong trend for higher incidence of MLL rearrangements and CD10-negative B-lineage ALL compared with older infants. Induction failure rate was 13% and not significantly different from that in older infants (7%, P = .14), but relapse rate was significantly higher in congenital ALL patients (2-year cumulative incidence [SE] was 60.0 [9.3] vs 34.2 [2.3], P < .001). Two-year event-free survival and survival of congenital ALL patients treated with this protocol was 20% (SE 9.1%). Early death in complete remission and treatment delays resulting from toxicity were not different. The survival of 17% after last follow-up, combined with a toxicity profile comparable with that in older infants, justifies treating congenital ALL with curative intent. This trial was registered at www.clinicaltrials.gov as no. NCT 00015873, and at www.controlled-trials.com as no. ISRCTN24251487.
Selective depletion of alloreactive T cells by targeted therapy of heat shock protein 90: a novel strategy for control of graft-versus-host disease
Authors: Stuehler Claudia , Mielke Stephan , Chatterjee Manik , Duell Johannes , Lurati Sarah , Rueckert Florian , Einsele Hermann , Bargou Ralf C. , Topp Max S. 
Published: August 2009

AbstractGraft-versus-host disease (GVHD) is a major cause of morbidity and mortality in patients with hematologic malignancies undergoing allogeneic hematopoietic stem cell transplantation. Current treatment of GVHD relies on immunosuppressive regimens, considerably increasing the incidence of opportunistic infections. As T cells mediate both GVHD as well as protection against viral infections and the malignant disease, strategies to selectively target host-reactive T cells without impairing pathogen- and disease-specific immunity are highly warranted. Activation of T cells is accompanied by increased expression of the chaperone heat shock protein of 90 kDa (Hsp90), which stabilizes several key signaling pathways crucial for T-cell activation. In this study, selective targeting of Hsp90 in activated T lymphocytes with pharmacologic inhibitors already applied successfully in anticancer therapy resulted in induction of apoptosis predominantly in activated cells. Moreover, if T cells were stimulated with allogeneic dendritic cells, alloreactive T cells were selectively eliminated. In contrast, third party reactions including antiviral T-cell immunity were quantitatively and functionally fully preserved. These data suggest that Hsp90 represents a novel target for selective depletion of alloreactive T cells, and provide the rationale for application of Hsp90 inhibitors as potential approach to selectively prevent and treat GVHD in hematopoietic stem cell transplantation recipients without impairing pathogen- and disease-specific T-cell immunity.
CSA: An efficient algorithm to improve circular DNA multiple alignment
Authors: Fernandes Francisco , Pereira Luísa , Freitas Ana T 
Published: August 2009

Abstract

Background
The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools.

Results
In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes.
To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView.

Conclusion
The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment algorithms when used in the alignment of circular DNA sequences. The resulting alignments lead to more realistic phylogenetic comparisons between species.
Phylogenetic distribution and membrane topology of the LytR-CpsA-Psr protein family
Authors: Hübscher Judith , Lüthy Lucas , Berger-Bächi Brigitte , Stutzmann Meier Patricia 
Published: August 2009

Abstract

Background
The bacterial cell wall is the target of many antibiotics and cell envelope constituents are critical to host-pathogen interactions. To combat resistance development and virulence, a detailed knowledge of the individual factors involved is essential. Members of the LytR-CpsA-Psr family of cell envelope-associated attenuators are relevant for β-lactam resistance, biofilm formation, and stress tolerance, and they are suggested to play a role in cell wall maintenance. However, their precise function is still unknown. This study addresses the occurrence as well as sequence-based characteristics of the LytR-CpsA-Psr proteins.

Results
A comprehensive list of LytR-CpsA-Psr proteins was established, and their phylogenetic distribution and clustering into subgroups was determined. LytR-CpsA-Psr proteins were present in all Gram-positive organisms, except for the cell wall-deficient Mollicutes and one strain of the Clostridiales. In contrast, the majority of Gram-negatives did not contain LytR-CpsA-Psr family members. Despite high sequence divergence, the LytR-CpsA-Psr domains of different subclusters shared a highly similar, predicted mixed a/β-structure, and conserved charged residues. PhoA fusion experiments, using MsrR of Staphylococcus aureus, confirmed membrane topology predictions and extracellular location of its LytR-CpsA-Psr domain.

Conclusion
The LytR-CpsA-Psr domain is unique to bacteria. The presence of diverse subgroups within the LytR-CpsA-Psr family might indicate functional differences, and could explain variations in phenotypes of respective mutants reported. The identified conserved structural elements and amino acids are likely to be important for the function of the domain and will help to guide future studies of the LytR-CpsA-Psr proteins.
Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome
Authors: Hamberger Björn , Hall Dawn , Yuen Mack , Oddy Claire , Hamberger Britta , Keeling Christopher I , Ritland Carol , Ritland Kermit , Bohlmann Jörg 
Published: August 2009

Abstract

Background
Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer.

Results
We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR) and a cytochrome P450 (CYP720B4) from a non-arrayed genomic BAC library of white spruce (Picea glauca). Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR) and 94 kbp (CYP720B4) long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs), high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing.

Conclusion
We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene families can be isolated in a gene-specific fashion. The results of the present work provide important new information about the structure and content of conifer genomic DNA that will guide future efforts to sequence and assemble conifer genomes.
Aberrant Expression of ID2 protein and its correlation with EBV-LMP1 and P16(INK4A) in Classical Hodgkin Lymphoma in China
Authors: Zhao Po , Lu Yali , Liu Lin , Zhong Mei 
Published: August 2009

Abstract

Background
The relationships between the expression of ID2, EBV-LMP1 and P16(INK4A) in Chinese classical Hodgkin lymphoma are unknown and need exploring.

Methods
Samples of classical Hodgkin lymphoma from 60 Chinese patients were analyzed for the expression of ID2, EBV-LMP1 and p16(INK4A) proteins by immunohistochemistry.

Results
ID2 protein was expressed in 83.3% of this group of classical Hodgkin lymphoma, staining strongly in both cytoplasm and nucleus of the Hodgkin and Reed-Sternberg (HRS) cells. EBV-LMP1 and P16(INK4A) were overexpressed in 85.0% and 71.7% of Hodgkin lymphoma, respectively. EBV-LMP1 was noted in the cytoplasm, membrane and nucleus of HRS cells; P16(INK4A) was in the nucleus and cytoplasm. Microscopically, ID2, EBV-LMP1 and P16(INK4A) staining distinguished the HRS cells from the complex background of lymphocytes. ID2 was positively correlated with EBV-LMP1(P < 0.01), but P16(INK4A) was inversely related to EBV-LMP1 (P < 0.05).

Conclusion
It is suggested that ID2, EBV-LMP1 and P16(INK4A) could play an important role in the evolution of classical Hodgkin lymphoma, and be considered as potential adjunct markers to identify HRS cells in diagnosis.
Gamma-phage lysin PlyG sequence-based synthetic peptides coupled with Qdot-nanocrystals are useful for developing detection methods for Bacillus anthracis by using its surrogates, B. anthracis-Sterne and B. cereus-4342
Authors: Sainathrao Shilpakala , Mohan Ketha V Krishna , Atreya Chintamani 
Published: August 2009

Abstract

Background
Previous reports of site-directed deletion analysis on gamma (γ)-phage lysin protein (PlyG) have demonstrated that removal of a short amino acid sequence in the C-terminal region encompassing a 10-amino acid motif (190LKMTADFILQ199) abrogates its binding activity specific to the cell wall of Bacillus anthracis. Whether short synthetic peptides representing the10-amino acid PlyG putative binding motif flanked by surrounding N- and C-terminal residues also selectively bind to the bacterial cell wall has not been evaluated. If such peptides do demonstrate selective binding to the cell wall, they could serve as bio-probes towards developing detection technologies for B. anthracis. Furthermore, by using B. anthracis (Sterne, 34F2), an animal vaccine and B. cereus-4342, a γ-phage susceptible rare strain as surrogates of B. anthracis, development of proof-of-concepts for B. anthracis are feasible.

Results
Using four different methods, we evaluated six synthetic peptides representing the putative binding motif including flanking sequences (PlyG-P1 through P6) for the bacterial cell wall binding capacity. Our analysis identified PlyG-P1, PlyG-P3 and PlyG-P5 to have binding capability to both B. anthracis (Sterne, 34F2) and B. cereus-4342. The peptides however did not bind to B. cereus-11778, B. thuringiensis, and B. cereus-10876 suggesting their specificity for B. anthracis-Sterne and B. cereus-4342. PlyG-P3 in combination with fluorescent light microscopy detected even a single bacterium in plasma spiked with the bacteria.

Conclusion
Overall, these studies illustrate that the short 10-amino acid sequence 'LKMTADFILQ' in fact is a stand-alone bacterial cell wall-binding motif of PlyG. In principle, synthetic peptides PlyG-P1, PlyG-P3 and PlyG-P5, especially PlyG-P3 coupled with Qdot-nanocrystals are useful as high-sensitivity bio-probes in developing detection technologies for B. anthracis.
Facial expression (mood) recognition from facial images using committee neural networks
Authors: Kulkarni Saket S , Reddy Narender P , Hariharan SI 
Published: August 2009

Abstract

Background
Facial expressions are important in facilitating human communication and interactions. Also, they are used as an important tool in behavioural studies and in medical rehabilitation. Facial image based mood detection techniques may provide a fast and practical approach for non-invasive mood detection. The purpose of the present study was to develop an intelligent system for facial image based expression classification using committee neural networks.

Methods
Several facial parameters were extracted from a facial image and were used to train several generalized and specialized neural networks. Based on initial testing, the best performing generalized and specialized neural networks were recruited into decision making committees which formed an integrated committee neural network system. The integrated committee neural network system was then evaluated using data obtained from subjects not used in training or in initial testing.

Results and conclusion
The system correctly identified the correct facial expression in 255 of the 282 images (90.43% of the cases), from 62 subjects not used in training or in initial testing. Committee neural networks offer a potential tool for image based mood detection.
Molecular genetics analysis of hereditary breast and ovarian cancer patients in India
Authors: Soumittra Nagasamy , Meenakumari Balaiah , Parija Tithi , Sridevi Veluswami , Nancy Karunakaran N , Swaminathan Rajaraman , Rajalekshmy Kamalalayam R , Majhi Urmila , Rajkumar Thangarajan 
Published: August 2009

Abstract

Background
Hereditary cancers account for 5–10% of cancers. In this study BRCA1, BRCA2 and CHEK2*(1100delC) were analyzed for mutations in 91 HBOC/HBC/HOC families and early onset breast and early onset ovarian cancer cases.

Methods
PCR-DHPLC was used for mutation screening followed by DNA sequencing for identification and confirmation of mutations. Kaplan-Meier survival probabilities were computed for five-year survival data on Breast and Ovarian cancer cases separately, and differences were tested using the Log-rank test.

Results
Fifteen (16%) pathogenic mutations (12 in BRCA1 and 3 in BRCA2), of which six were novel BRCA1 mutations were identified. None of the cases showed CHEK2*1100delC mutation. Many reported polymorphisms in the exonic and intronic regions of BRCA1 and BRCA2 were also seen. The mutation status and the polymorphisms were analyzed for association with the clinico-pathological features like age, stage, grade, histology, disease status, survival (overall and disease free) and with prognostic molecular markers (ER, PR, c-erbB2 and p53).

Conclusion
The stage of the disease at diagnosis was the only statistically significant (p < 0.0035) prognostic parameter. The mutation frequency and the polymorphisms were similar to reports on other ethnic populations. The lack of association between the clinico-pathological variables, mutation status and the disease status is likely to be due to the small numbers.
Endotoxin tolerance dysregulates MyD88- and Toll/IL-1R domain-containing adapter inducing IFN-β-dependent pathways and increases expression of negative regulators of TLR signaling
Authors: Piao Wenji , Song Chang , Chen Haiyan , Quevedo Diaz Marco A , Wahl Larry M , Fitzgerald Katherine A , Li Liwu , Medvedev Andrei E 
Published: August 2009

Abstract
Endotoxin tolerance interferes with TLR4 signalosome assembly, kinase/transcription factor activation, and increases negative TLR pathway regulators.
Endotoxin tolerance reprograms cell responses to LPS by repressing expression of proinflammatory cytokines, while not inhibiting production of anti-inflammatory cytokines and antimicrobial effectors. Molecular mechanisms of induction and maintenance of endotoxin tolerance are incompletely understood, particularly with regard to the impact of endotoxin tolerization on signalosome assembly, activation of adaptor-kinase modules, and expression of negative regulators of TLR signaling in human cells. In this study, we examined LPS-mediated activation of MyD88-dependent and Toll-IL-1R-containing adaptor inducing IFN-β (TRIF)-dependent pathways emanating from TLR4 and expression of negative regulators of TLR signaling in control and endotoxin-tolerant human monocytes. Endotoxin tolerization suppressed LPS-inducible TLR4-TRIF and TRIF-TANK binding kinase (TBK)1 associations, induction of TBK1 kinase activity, activation of IFN regulatory factor (IRF)-3, and expression of RANTES and IFN-β. Tolerance-mediated dysregulation of the TLR4-TRIF-TBK1 signaling module was accompanied by increased levels of suppressor of IκB kinase-ε (SIKE) and sterile α and Armadillo motif-containing molecule (SARM). LPS-tolerant cells showed increased expression of negative regulators Toll-interacting protein (Tollip), suppressor of cytokine signaling (SOCS)-1, IL-1R-associated kinase-M, and SHIP-1, which correlated with reduced p38 phosphorylation, IκB-α degradation, and inhibited expression of TNF-α, IL-6, and IL-8. To examine functional consequences of increased expression of Tollip in LPS-tolerized cells, we overexpressed Tollip in 293/TLR4/MD-2 transfectants and observed blunted LPS-inducible activation of NF-κB and RANTES, while TNF-α responses were not affected. These data demonstrate dysregulation of TLR4-triggered MyD88- and TRIF-dependent signaling pathways and increased expression of negative regulators of TLR signaling in endotoxin-tolerant human monocytes.
Formation of Specific Charge-transfer Complexes between Hyperbranched Polymer Viologen and Neutral Donors in Solid Films Depending on Donor Fraction
Authors: Sakano Takeshi , Ito Fuyuki , Hirata Osamu , Ozawa Masaaki , Nagamura Toshihiko 
Published: August 2009

Abstract
Neutral donors and hyperbranched polymer with many viologen groups formed charge-transfer complexes in solutions and solid films. The charge-transfer absorption and fluorescence spectra showed red shifts with increasing donor fractions only in the case of polymer solid films, strongly suggesting solvatochromism in solid films and formation of multichromophore CT complex. These are unique microenvironmental effects of the present cationic polymer.
Post-synthesis Emission Control of CdSe–ZnS Quantum Dots by Surface Oxidation through In Situ Generation of Oxidant under Mild Reaction Conditions
Authors: Kim Yong Tae , Kim Jae Il , Lee Jin-Kyu , Chae Hee K 
Published: August 2009

Abstract
We proposed in situ generation of cyclohexenyl peroxide as a surface oxidant in solution of CdSe quantum dots and verified it by monitoring emission wavelengths and intensities of CdSe and CdSe–ZnS in cyclohexene, respectively. A clear 80 nm blue shift in the emission was observed in CdSe–ZnS over 3 mon due to the slow diffusion of the oxidant, while a 10 nm shift was in CdSe for 24 h.