bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epithelial and Stromal Cathepsin K and CXCL14 Expression in Breast Tumor Progression
Authors: Kleer Celina G. , Bloushtain-Qimron Noga , Chen Yu-Hui , Carrasco Daniel , Hu Min , Yao Jun , Kraeft Stine-Kathrein , Collins Laura C. , Sabel Michael S. , Argani Pedram , Gelman Rebecca , Schnitt Stuart J. , Krop Ian E. , Polyak Kornelia 
Published: September 2008

Abstract
Purpose: To evaluate the expression of cathepsin K (CTSK) and CXCL14 in stromal and epithelial cells in human breast tumor progression.
Experimental Design: We did immunohistochemical analyses of CTSK and CXCL14 expression in normal breast tissue, biopsy sites, benign lesions, ductal carcinoma in situ, and invasive breast tumors of different stages. Expression patterns were related to histopathologic characteristics of the tumors and clinical outcome. The effect of CTSK+ breast stromal fibroblasts on CTSK- breast cancer cells was assessed in coculture.
Results: Epithelial expression of CTSK was rarely detected in any of the tissue samples analyzed, whereas CXCL14-positive epithelial cells were found in all tissue types. The expression of CXCL14 was not associated with any tumor or patient characteristics analyzed. Stromal CTSK expression was significantly higher in invasive compared with in situ carcinomas, and in one of the two data sets analyzed, it correlated with higher tumor stage. Among all samples examined, the highest stromal CTSK levels were detected in biopsy sites. Neither epithelial nor stromal expression of CTSK was significantly associated with recurrence-free or overall survival. Coculture of CTSK+ fibroblasts enhanced the invasion of CTSK- breast tumor epithelial cells and this was blocked by CTSK inhibitors.
Conclusions: CTSK may function as a paracrine factor in breast tumorigenesis. CTSK+ fibroblasts may play a role in tumor progression by promoting the invasiveness of tumor epithelial cells. The possibility that CTSK inhibitors may have a clinical role in decreasing the risk of tumor progression merits further investigation.
β2-Microglobulin Signaling Blockade Inhibited Androgen Receptor Axis and Caused Apoptosis in Human Prostate Cancer Cells
Authors: Huang Wen-Chin , Havel Jonathan J. , Zhau Haiyen E. , Qian Wei Ping , Lue Hui-Wen , Chu Chia-Yi , Nomura Takeo , Chung Leland W.K. 
Published: September 2008

AbstractPurpose: β2-Microglobulin (β2M) has been shown to promote osteomimicry and the proliferation of human prostate cancer cells. The objective of this study is to determine the mechanism by which targeting β2M using anti-β2M antibody inhibited growth and induced apoptosis in prostate cancer cells.Experimental Design: Polyclonal and monoclonal β2M antibodies were used to interrupt β2M signaling in human prostate cancer cell lines and the growth of prostate tumors in mice. The effects of the β2M antibody on a survival factor, androgen receptor (AR), and its target gene, prostate-specific antigen (PSA) expression, were investigated in cultured cells and in tumor xenografts.Results: The β2M antibody inhibited growth and promoted apoptosis in both AR-positive and PSA-positive, and AR-negative and PSA-negative, prostate cancer cells via the down-regulation of the AR in AR-positive prostate cancer cells and directly caused apoptosis in AR-negative prostate cancer cells in vitro and in tumor xenografts. The β2M antibody had no effect on AR expression or the growth of normal prostate cells.Conclusions: β2M downstream signaling regulates AR and PSA expression directly in AR-positive prostate cancer cells. In both AR-positive and AR-negative prostate cancer cells, interrupting β2M signaling with the β2M antibody inhibited cancer cell growth and induced its apoptosis. The β2M antibody is a novel and promising therapeutic agent for the treatment of human prostate cancers.
Hierarchical fibre composite structure and micromechanical properties of phosphatic and calcitic brachiopod shell biomaterials — an overview
Authors: Schmahl W. W. , Griesshaber E. , Merkel C. , Kelm K. , Deuschle J. , Neuser R. D. , Göetz A. J. , Sehrbrock A. , Mader W. 
Published: September 2008

AbstractBrachiopods are a phylum of shell-forming sessile marine invertebrates which have existed since the early Cambrian. Two very different biomaterial design strategies for their shells evolved early in their history. Both strategies use hybrid fibre composites, however, one is based on mineral fibres embedded in ~2 wt.% of organic biopolymer sheaths and the inorganic fibres are calcite single crystals. In the second strategy the fibres are biopolymers and are reinforced with Ca-phosphate nanoparticles to form a fibrous nanocomposite. Here the organic component (chitin) dominates. The Ca-phosphate nanoparticle-reinforcement strategy is not unlike that in vertebrate bone, however, the microscale structure is laminated with alternating laminae which have a different degree of mineralization.The calcitic shells feature an outer compact layer of calcite micro- and nanoparticles protecting the inner fibrous layer from the outside. Transmission electron microscopy of the fibrous layer reveals intercrystalline and intracrystalline biopolymers. The calcitic shell material is stiff with nano-indentation E-moduli of 63±8 GPa and relatively hard (Vickers microhardness up to 400 HV 0.0005/10 and nanohardness 4±0.5 GPa). Compared to inorganic calcite the microhardness is doubled and the nanohardness increases by 60%. We attribute this increased hardness to intracrystalline biopolymers. The nano-indentation E-moduli of the chitinophosphatic shells range from 3 to 55 GPa as a result of the varying degree of mineralization between their laminae, and similarly their nanohardness varies between 0.1 and 3 GPa. For brachiopods burrowing inside the sediment, the alternation of non-mineralized laminae with thin, more strongly mineralized laminae provides abrasion-resistance, hardness and longitudinal stiffness while it preserves the flexibility provided by the organic component for bending movements.
Assessment of crystallographic influence on material properties of calcite brachiopods
Authors: Pérez-Huerta A. , Cusack M. , Zhu W. 
Published: September 2008

AbstractCalcium carbonate biominerals are frequently analysed in materials science due to their abundance, diversity and unique material properties. Aragonite nacre is intensively studied, but less information is available about the material properties of biogenic calcite, despite its occurrence in a wide range of structures in different organisms. In particular, there is insufficient knowledge about how preferential crystallographic orientations influence these material properties. Here, we study the influence of crystallography on material properties in calcite semi-nacre and fibres of brachiopod shells using nanoindentation and electron backscatter diffraction (EBSD). The nano-indentation results show that calcite semi-nacre is a harder and stiffer (H ≈ 3—5 GPa; E = 50–85 GPa) biomineral structure than calcite fibres (H = 0.4—3 GPa; E = 30—60 GPa). The integration of EBSD to these studies has revealed a relationship between the crystallography and material properties at high spatial resolution for calcite semi-nacre. The presence of crystals with the c-axis perpendicular to the plane-of-view in longitudinal section increases hardness and stiffness. The present study determines how nano-indentation and EBSD can be combined to provide a detailed understanding of biomineral structures and their analysis for application in materials science.
Oxygen isotope composition inModiolus modiolusaragonite in the context of biological and crystallographic control
Authors: Cusack M. , Parkinson D. , Freer A. , Pérez-Huerta A. , Fallick A. E. , Curry G. B. 
Published: September 2008

AbstractLiving systems exert exquisite control on all aspects of biomineral production and organic components, including proteins, are essential to this biological control. The protein-rich extrapallial (EP) fluid of bivalve molluscs is a strong candidate for the source of such proteins. Differences in calcium carbonate polymorphs betweenModiolus modiolusandMytilus edulisare concurrent with differences in EP fluid protein profiles. In conjunction with this biological control is the environmental influence which is interpreted using proxies such as δ18O to determine the history of ambient seawater temperature. In the horse mussel,Modiolus modiolus, the difference in oxygen isotope fractionation in the nacreous aragonite and the prismatic aragonite layer results in respective δ18O values of 2.1±0.2% and 2.5±0.2%. These δ18O values result in estimates of ambient seawater of 12.1±0.6°C and 10.2±0.6°C for nacreous and prismatic aragonite, respectively. Electron backscatter diffraction is used here to determine the crystallographic orientation at high spatial resolution, allowing the measurements of stable isotopes to be accurately mapped in terms of shell architecture. These preliminary data suggest that it is essential to account for both polymorph and crystal habit when deciphering ambient seawater temperature using δ18O as a proxy.
Structural characterization and chemical composition of aragonite and vaterite in freshwater cultured pearls
Authors: Soldati A. L. , Jacob D. E. , Wehrmeister U. , Hofmeister W. 
Published: September 2008

AbstractVaterite and aragonite polymorphs in freshwater cultured pearls from mussels of the genus Hyriopsis (Unionidae) were structurally and compositionally characterized by Raman spectroscopy, Micro computer tomography, high resolution field emission scanning electron microscopy, electron microprobe analysis and laser ablation inductively coupled plasma mass spectrometry. The appearance of vaterite in pearls is related to the initial stages of biomineralization, although we demonstrate that vaterite can not be a precursor to aragonite. It is not related to a particular crystal habit and therefore does not have a structural functionality in the pearls. Larger contents of elements typically bound to organic molecules, such as P and S in vaterite, as well as larger total organic contents in vaterite as opposed to aragonite in conjunction with larger concentrations of Mn2+ and Mg2+, imply a stabilizing role of organic macromolecules and X2+ ions for biological vaterite. Distribution coefficients between aragonite and vaterite for provenance-independent elements, such as Mn and Mg (0.27 and 0.04, respectively) agree very well with those observed in fish otoliths.
Trace-element distributions in fish otoliths: natural markers of life histories, environmental conditions and exposure to tailings effluence
Authors: Halden N. M. , Friedrich L. A. 
Published: September 2008

AbstractOtoliths, the earbones of teleost (bony) fish, are constructed from alternating layers of aragonite and protein. Laser ablation inductively coupled plasma mass spectrometry and proton-induced X-ray emission are used to obtain spatially well-resolved trace element line-scans that show trace-element concentrations are correlated with the annular structure. Zoned Sr and Zn signatures are common whereas other elements such as Cu, Pb, Li and Cs can be related to the proximity of mineral deposits. Aragonite in otoliths can incorporate a wide range of trace elements at the low-ppm level including alkali- and alkaline-earth elements and base metals; Se has also been detected in proximity to coal mines. These trace elements, in combination with the annular structures, are an important archive for recording information on environments occupied by fish, environmental change and exposure to pollutants.
Crystallization of biogenic Ca-carbonate within organo-mineral micro-domains. Structure of the calcite prisms of the PelecypodPinctada margaritifera(Mollusca) at the submicron to nanometre ranges
Authors: Baronnet A. , Cuif J. P. , Dauphin Y. , Farre B. , Nouet J. 
Published: September 2008

AbstractAtomic force microscopy (AFM) and transmission electron microscopy (TEM) were used to investigate the fine structure of the calcite prisms from the pearl-oyster shellPinctada margaritifera. The AFM analysis shows that the prisms are made of densely packed circular micro-domains (in the 0.1 μm range) surrounded by a dense cortex. The TEM images and diffraction patterns allow the internal structure of the micro-domains to be described. Each of them is enriched in Ca-carbonate. Hosted in distinct regions of each prism, some are fully amorphous, and some others fully crystallized as subunits of a large calcite single crystal. At the border separating the two regions, micro-domains display a crystallized core and an amorphous rim. Such a border probably marks out an arrested crystallization front having propagated through a previously bio-controlled architecture of the piling of amorphous micro-domains. Compared to recent data concerning the stepping mode of growth of the calcite prisms and the resulting layered organization at the μm-scale, these results give unexpected views regarding the modalities of biocrystallization.
Mineralogical approaches to the study of biomineralization in fish otoliths
Authors: Melancon S. , Fryer B. J. , Gagnon J. E. , Ludsin S. A. 
Published: September 2008

AbstractThis paper highlights new research on the biomineralization of otoliths and uses a mineralogical approach to understand mechanisms of crystal growth and metal incorporation into otoliths. Petrographic observations of the nucleation of otolith growth in the core for several fish species reveals that sagittal otoliths appear to nucleate around a few or many nucleation sites (primordia) and that these sites vary in size (ranging in diameter from 1 to 20 μm), depending on the species. Spectroscopic data show a large Mn-enrichment in the primordia within the core but the reasons for this enrichment are still unclear (e.g. organic matter or possibly another material other than CaCO3). This study also provides the first multi trace-element data for endolymph fluid and the growing otolith; we found large enrichments (Ca and Sr) and depletions (Na, K, Zn and Rb) of elements in the otolith relative to the endolymph. The last part of this paper examines the effect of crystal structure on the microchemistry ofotoliths. Our investigation helps understand how the chemical characteristics of the metal ions (i.e. ionic radii) and the crystalline structure interact to cause differential trace-metal uptake between the CaCO3polymorphs, aragonite and vaterite.
Biological enhancement of soil carbonate precipitation: passive removal of atmospheric CO2
Authors: Manning D. A. C. 
Published: September 2008

AbstractSoils are the dominant terrestrial sink for carbon, containing three times as much C as above-ground plant biomass, and acting as a host for both organic and inorganic C, as soil organic matter and pedogenic carbonates, respectively. This article reviews evidence for the generation within the soil solution of dissolved C derived from plants and recognition of its precipitation as carbonates. It then considers the potential value of this process for artificially-mediated CO2 sequestration within soils. The ability of crops such as wheat to produce organic acid anions as root exudates is substantial, generating 70 mol/(y kg) of exuded C, equivalent to the plant's own ‘body weight’. This is still an order of magnitude less than measured C production from Icelandic woodlands (Moulton et al., 2000), which have no other possible source of C. Thus, there is apparently no shortage of available dissolved C, as bicarbonate in solution, and so the formation of pedogenic carbonates will be controlled by the availability of Ca. This is derived from mineral weathering, primarily of silicate minerals (natural plagioclase feldspars and pyroxenes; artificial cement and slag minerals). Within the UK, existing industrial arisings of calcium silicate minerals from quarrying, demolition and steel manufacture that are fine-grained and suitable for incorporation into soils are sufficient to account for 3 MT CO2 per year, compensating for half of the emissions from UK cement manufacture. Pursuing these arguments, it is shown that soils have a role to play as passive agents in the removal of atmospheric CO2, analogous to the use of reed beds to clean contaminated waters.
Phase transitions of BaCO3 at high pressures
Authors: Ono S. , Brodholt J. P. , Price G. D. 
Published: September 2008

AbstractFirst-principles simulations and high-pressure experiments were used to study the stability of BaCO3 carbonates at high pressures. Witherite, which is orthorhombic and isotypic with CaCO3 aragonite, is stable at ambient conditions. As pressure increases, BaCO3 transforms from witherite to an orthorhombic post-aragonite structure at 8 GPa. The calculated bulk modulus of the post-aragonite structure is 60.7 GPa, which is slightly less than that from experiments. This structure shows an axial anisotropicc ompressibility and the a axis intersects with the c axis at 70 GPa, which implies that the pressure-induced phase transition reported in previous experimental study is misidentified. Although a pyroxene-like structure is stable in Mg- and Ca-carbonates at pressures >100 GPa, our simulations showed that this structure does not appear in BaCO3.
In situ X-ray absorption spectroscopy measurement of vapour-brine fractionation of antimony at hydrothermal conditions
Authors: Pokrovski G. S. , Roux J. , Hazemann J.-L. , Borisova A. YU. , Gonchar A. A. , Lemeshko M. P. 
Published: September 2008

AbstractDespite the growing geological evidence that fluid boiling and vapour-liquid separation affect the distribution of metals in magmatic-hydrothermal systems significantly, there are few experimental data on the chemical status and partitioning of metals in the vapour and liquid phases. Here we report on an in situ measurement, using X-ray absorption fine structure (XAFS) spectroscopy, of antimony speciation and partitioning in the system Sb2O3-H2O-NaCl-HCl at 400°C and pressures 270—300 bar corresponding to the vapour-liquid equilibrium. Experiments were performed using a spectroscopic cell which allows simultaneous determination of the total concentration and atomic environment of the absorbing element (Sb) in each phase. Results show that quantitative vapour-brine separation of a supercritical aqueous salt fluid can be achieved by a controlled decompression and monitoring the X-ray absorbance of the fluid phase. Antimony concentrations in equilibrium with Sb2O3 (cubic, senarmontite) in the coexisting vapour and liquid phases and corresponding SbIII vapour-liquid partitioning coefficients are in agreement with recent data obtained using batch-reactor solubility techniques. The XAFS spectra analysis shows that hydroxy-chloride complexes, probably Sb(OH)2Cl0, are dominant both in the vapour and liquid phase in a salt-water system at acidic conditions. This first in situ XAFS study of element fractionation between coexisting volatile and dense phases opens new possibilities for systematic investigations of vapour-brine and fluid-melt immiscibility phenomena, avoiding many experimental artifacts common in less direct techniques.
Impact of residue accessible surface area on the prediction of protein secondary structures
Authors: Momen-Roknabadi Amir , Sadeghi Mehdi , Pezeshk Hamid , Marashi Sayed-Amir 
Published: September 2008

AbstractBackgroundThe problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibility (RSA) might be an effective factor for increasing the accuracy of protein secondary structure prediction. Previous studies have either used a single constant threshold to classify residues into discrete classes (buries vs. exposed), or used the real-value predicted RSAs in their prediction method.ResultsWe studied the effect of applying different RSA threshold types (namely, fixed thresholds vs. residue-dependent thresholds) on a variety of secondary structure prediction methods. With the consideration of DSSP-assigned RSA values we realized that improvement in the accuracy of prediction strictly depends on the selected threshold(s). Furthermore, we showed that choosing a single threshold for all amino acids is not the best possible parameter. We therefore used residue-dependent thresholds and most of residues showed improvement in prediction. Next, we tried to consider predicted RSA values, since in the real-world problem, protein sequence is the only available information. We first predicted the RSA classes by RVP-net program and then used these data in our method. Using this approach, improvement in prediction was also obtained.ConclusionThe success of applying the RSA information on different secondary structure prediction methods suggest that prediction accuracy can be improved independent of prediction approaches. Thus, solvent accessibility can be considered as a rich source of information to help the improvement of these methods.
Methodology capture: discriminating between the "best" and the rest of community practice
Authors: Eales James M , Pinney John W , Stevens Robert D , Robertson David L 
Published: September 2008

Abstract

Background
The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable protocols in a specific research area. To remedy this we present an approach for capturing methodology from literature in order to identify and, thus, define best practice within a field.

Results
Our approach is to implement data extraction techniques on the full-text of scientific articles to obtain the set of experimental protocols used by an entire scientific discipline, molecular phylogenetics. Our methodology for identifying methodologies could in principle be applied to any scientific discipline, whether or not computer-based. We find a number of issues related to the nature of best practice, as opposed to community practice. We find that there is much heterogeneity in the use of molecular phylogenetic methods and software, some of which is related to poor specification of protocols. We also find that phylogenetic practice exhibits field-specific tendencies that have increased through time, despite the generic nature of the available software. We used the practice of highly published and widely collaborative researchers ("expert" researchers) to analyse the influence of authority on community practice. We find expert authors exhibit patterns of practice common to their field and therefore act as useful field-specific practice indicators.

Conclusion
We have identified a structured community of phylogenetic researchers performing analyses that are customary in their own local community and significantly different from those in other areas. Best practice information can help to bridge such subtle differences by increasing communication of protocols to a wider audience. We propose that the practice of expert authors from the field of evolutionary biology is the closest to contemporary best practice in phylogenetic experimental design. Capturing best practice is, however, a complex task and should also acknowledge the differences between fields such as the specific context of the analysis.