bluuebunny/crossref_metadata_2025_split huggingface dataset:
APRIL promotes cell-cycle progression in primary multiple myeloma cells: influence of D-type cyclin group and translocation status
Authors: Quinn John , Glassford Janet , Percy Laura , Munson Philippa , Marafioti Teresa , Rodriguez-Justo Manuel , Yong Kwee 
Published: August 2010

Abstract
A proliferation-inducing ligand (APRIL) promotes survival and drug resistance in multiple myeloma (MM) cell lines. We studied the effect of APRIL on cell-cycle behavior in primary MM cells and correlated our findings with D-type cyclin expression by immunohistochemistry and/or Western blotting. In MM cases, expressing cyclin D2 APRIL significantly increased the percentage of CD138+ cells in S + G2/M phase (from 8.4% ± 1.9% to 14.3% ± 2.6%, n = 15, P < .01), whereas a lesser effect was seen in cases expressing cyclin D1 (n = 18). Cell-cycle response to APRIL was most marked for cyclin D2-expressing cases with IgH translocations (P < .01) and was accompanied by increased expression of cyclin D2, CDK4, CDK6, and phospho-retinoblastoma protein. Cell-cycle proteins in cyclin D1+ cells were not modulated by APRIL. Surface expression of B-cell maturation antigen and transmembrane activator and calcium-modulating cyclophilin ligand interactor was not significantly different between cyclin D1+ and D2+ MM cells. We observed activation of nuclear factor-κB and PI3-kinase pathways in response to APRIL in both cyclin D1+ and D2+ MM cells. In conclusion, APRIL stimulates G1/S progression in cyclin D2+ MM cells bearing IgH translocations but has minimal effect on cyclin D1+ cells, suggesting MM cells from different cyclin D/translocation classes rely on different mechanisms for cell-cycle re-entry.
Design and characterization of a cleavage-resistant Annexin A1 mutant to control inflammation in the microvasculature
Authors: Pederzoli-Ribeil Magali , Maione Francesco , Cooper Dianne , Al-Kashi Adam , Dalli Jesmond , Perretti Mauro , D'Acquisto Fulvio 
Published: August 2010

AbstractHuman polymorphonuclear leukocytes adhesion to endothelial cells during the early stage of inflammation leads to cell surface externalization of Annexin A1 (AnxA1), an effector of endogenous anti-inflammation. The antiadhesive properties of AnxA1 become operative to finely tune polymorphonuclear leukocytes transmigration to the site of inflammation. Membrane bound proteinase 3 (PR3) plays a key role in this microenvironment by cleaving the N terminus bioactive domain of AnxA1. In the present study, we generated a PR3-resistant human recombinant AnxA1—named superAnxA1 (SAnxA1)—and tested its in vitro and in vivo properties in comparison to the parental protein. SAnxA1 bound and activated formyl peptide receptor 2 in a similar way as the parental protein, while showing a resistance to cleavage by recombinant PR3. SAnxA1 retained anti-inflammatory activities in the murine inflamed microcirculation (leukocyte adhesion being the readout) and in skin trafficking model. When longer-lasting models of inflammation were applied, SAnxA1 displayed stronger anti-inflammatory effect over time compared with the parental protein. Together these results indicate that AnxA1 cleavage is an important process during neutrophilic inflammation and that controlling the balance between AnxA1/PR3 activities might represent a promising avenue for the discovery of novel therapeutic approaches.
Effect of FCGR2A and FCGR3A variants on CLL outcome
Authors: Dornan David , Spleiss Olivia , Yeh Ru-Fang , Duchateau-Nguyen Guillemette , Dufour Annika , Zhi Jianguo , Robak Tadeusz , Moiseev Sergey I. , Dmoszynska Anna , Solal-Celigny Philippe , Warzocha Krzysztof , Loscertales Javier , Catalano John , Afanasiev Boris V. , Larratt Loree , Rossiev Viktor A. , Bence-Bruckler Isabelle , Geisler Christian H. , Montillo Marco , Wenger Michael K. , Weisser Martin 
Published: August 2010

AbstractPolymorphisms of activating Fc-γ receptors (FCGRs) on natural killer cells and macrophages result in variable affinity for immunoglobulin G1 monoclonal antibodies and subsequently modulate antibody-dependent cellular cytotoxicity (ADCC) activity. Whether single-nucleotide polymorphisms of FCGRs correlate with survival of chronic lymphocytic leukemia (CLL) patients treated with a monoclonal antibody containing regimen is unclear. We assessed the FCGR3A and FCGR2A genotype of patients enrolled in the REACH trial, where patients received fludarabine and cyclophosphamide (FC) or rituximab plus FC (R-FC). FCGR3A and FCGR2A polymorphisms did not demonstrate prognostic significance in the FC arm (P = .42 and P = .64, respectively) or R-FC arm (P = .41 and P = .88, respectively) with respect to progression free survival. Patients with intermediate affinity genotypes (FV and HR) benefited significantly from addition of rituximab (hazard ratio = 0.55 [0.37-0.8 CI]; P = .0017 and hazard ratio = 0.63 [0.44-0.9 CI]; P = .011, respectively). Similar benefit was suggested for patients with high- affinity VV and HH (hazard ratio = 0.86 [0.4-1.84 CI]; P = .7 and hazard ratio = 0.7 [0.41-1.18 CI]; P = .18, respectively) and low-affinity FF and RR (hazard ratio = 0.85 [0.56-1.29 CI]; P = .44 and hazard ratio = 0.82 [0.47-1.42 CI]; P = .48, respectively). Overall, our results suggest that FCGR2A and FCGR3A polymorphisms do not significantly influence the outcomes of relapsed or refractory CLL patients treated with FC or the monoclonal antibody regimen R-FC.
TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base
Authors: Cui Xiaoqi , Wang Tong , Chen Huann-Sheng , Busov Victor , Wei Hairong 
Published: August 2010

Abstract

Background
Identification of transcription factors (TFs) involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a large number of genes and complicated interactions in a gene regulatory network (GRN), identification of the TFs involved in a biology process remains to be very challenging. In reality, the recognition of TFs for a given a biological process can be further complicated by the fact that most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation except for small conserved domains. This poses a significant challenge for identification of the exact TFs involved or ranking the importance of a set of TFs to a process of interest. Therefore, new methods for recognizing novel TFs are desperately needed. Although a plethora of methods have been developed to infer regulatory genes using microarray data, it is still rare to find the methods that use existing knowledge base in particular the validated genes known to be involved in a process to bait/guide discovery of novel TFs. Such methods can replace the sometimes-arbitrary process of selection of candidate genes for experimental validation and significantly advance our knowledge and understanding of the regulation of a process.

Results
We developed an automated software package called TF-finder for recognizing TFs involved in a biological process using microarray data and existing knowledge base. TF-finder contains two components, adaptive sparse canonical correlation analysis (ASCCA) and enrichment test, for TF recognition. ASCCA uses positive target genes to bait TFS from gene expression data while enrichment test examines the presence of positive TFs in the outcomes from ASCCA. Using microarray data from salt and water stress experiments, we showed TF-finder is very efficient in recognizing many important TFs involved in salt and drought tolerance as evidenced by the rediscovery of those TFs that have been experimentally validated. The efficiency of TF-finder in recognizing novel TFs was further confirmed by a thorough comparison with a method called Intersection of Coexpression (ICE).

Conclusions
TF-finder can be successfully used to infer novel TFs involved a biological process of interest using publicly available gene expression data and known positive genes from existing knowledge bases. The package for TF-finder includes an R script for ASCCA, a Perl controller, and several Perl scripts for parsing intermediate outputs. The package is available upon request (hairong@mtu.edu). The R code for standalone ASCCA is also available.
Ultraviolet stress delays chromosome replication in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511
Authors: Kolowrat Christian , Partensky Frédéric , Mella-Flores Daniella , Le Corguillé Gildas , Boutte Christophe , Blot Nicolas , Ratin Morgane , Ferréol Martial , Lecomte Xavier , Gourvil Priscillia , Lennon Jean-François , Kehoe David M , Garczarek Laurence 
Published: August 2010

Abstract

Background
The marine cyanobacterium Prochlorococcus is very abundant in warm, nutrient-poor oceanic areas. The upper mixed layer of oceans is populated by high light-adapted Prochlorococcus ecotypes, which despite their tiny genome (~1.7 Mb) seem to have developed efficient strategies to cope with stressful levels of photosynthetically active and ultraviolet (UV) radiation. At a molecular level, little is known yet about how such minimalist microorganisms manage to sustain high growth rates and avoid potentially detrimental, UV-induced mutations to their DNA. To address this question, we studied the cell cycle dynamics of P. marinus PCC9511 cells grown under high fluxes of visible light in the presence or absence of UV radiation. Near natural light-dark cycles of both light sources were obtained using a custom-designed illumination system (cyclostat). Expression patterns of key DNA synthesis and repair, cell division, and clock genes were analyzed in order to decipher molecular mechanisms of adaptation to UV radiation.

Results
The cell cycle of P. marinus PCC9511 was strongly synchronized by the day-night cycle. The most conspicuous response of cells to UV radiation was a delay in chromosome replication, with a peak of DNA synthesis shifted about 2 h into the dark period. This delay was seemingly linked to a strong downregulation of genes governing DNA replication (dnaA) and cell division (ftsZ, sepF), whereas most genes involved in DNA repair (such as recA, phrA, uvrA, ruvC, umuC) were already activated under high visible light and their expression levels were only slightly affected by additional UV exposure.

Conclusions

Prochlorococcus cells modified the timing of the S phase in response to UV exposure, therefore reducing the risk that mutations would occur during this particularly sensitive stage of the cell cycle. We identified several possible explanations for the observed timeshift. Among these, the sharp decrease in transcript levels of the dnaA gene, encoding the DNA replication initiator protein, is sufficient by itself to explain this response, since DNA synthesis starts only when the cellular concentration of DnaA reaches a critical threshold. However, the observed response likely results from a more complex combination of UV-altered biological processes.
Elasticity and stress relaxation of rhesus monkey (Macaca mulatta) vocal folds
Authors: Riede Tobias 
Published: August 2010

SUMMARYFundamental frequency is an important perceptual parameter for acoustic communication in mammals. It is determined by vocal fold oscillation, which depends on the morphology and viscoelastic properties of the oscillating tissue. In this study, I tested if stress–strain and stress–relaxation behavior of rhesus monkey (Macaca mulatta) vocal folds allows the prediction of a species' natural fundamental frequency range across its entire vocal repertoire as well as of frequency contours within a single call type. In tensile tests, the load–strain and stress–relaxation behavior of rhesus monkey vocal folds and ventricular folds has been examined. Using the string model, predictions about the species' fundamental frequency range, individual variability, as well as the frequency contour of ‘coo’ calls were made. The low- and mid-frequency range (up to 2 kHz) of rhesus monkeys can be predicted relatively well with the string model. The discrepancy between predicted maximum fundamental frequency and what has been recorded in rhesus monkeys is currently ascribed to the difficulty in predicting the behavior of the lamina propria at very high strain. Histological sections of the vocal fold and different staining techniques identified collagen, elastin, hyaluronan and, surprisingly, fat cells as components of the lamina propria. The distribution of all four components is not uniform, suggesting that different aspects of the lamina propria are drawn into oscillation depending on vocal fold tension. A differentiated recruitment of tissue into oscillation could extend the frequency range specifically at the upper end of the frequency scale.
Expression and role of the cell surface protease seprase/fibroblast activation protein-α (FAP-α) in astroglial tumors
Authors: Mentlein Rolf , Hattermann Kirsten , Hemion Charles , Jungbluth Achim A. , Held-Feindt Janka 
Published: August 2010

Abstract
Seprase or fibroblast activation protein-α (FAP-α) is a cell-surface serine protease that was previously described nearly exclusively on reactive and tumor stromal fibroblasts and thought to be involved in tissue remodeling. We investigated the expression and significance of FAP-α in astrocytomas/glioblastomas. As shown by quantitative reverse transcription polymerase chain reaction (RT-PCR) and immunohisto-chemistry, FAP-α was elevated in whole glioblastoma tissues and in particular in most glioma cells in situ and in vitro. In glioma stem-like cells (gliospheres), FAP-α was detected at low levels; however, FAP-α was considerably induced upon differentiation with 10% fetal calf serum. To explore its functional role, FAP-α was silenced by siRNA transfection. In Boyden chamber assays, FAP-α silenced cells migrated similar as control cells through non-coated or Matrigel (basal lamina)-coated porous membranes, but significantly slower through membranes coated with gelatin or brevican, a major component of brain extracellular matrix. Furthermore, FAP-α-silenced glioma cells migrated through murine brain slices much slower under the conditions tested than differentially fluorescent-labeled control cells. Thus, FAP-α is highly expressed on the surface of glioma cells and contributes to diffuse glioma invasion through extracellular matrix components.
Automated assay for non-transferrin-bound iron in serum samples
Authors: Prezelj Marija , Knap Bojan 
Published: August 2010

Abstract

Background: Non-transferrin-bound iron (NTBI) is a powerful promoter of free radical damage and highly toxic to biological systems, resulting in oxidative damage to proteins, lipids and DNA.

Methods: This assay is based on the binding of serum NTBI by the chelator nitrilotriacetic acid (NTA) and measurement of the ultrafiltrated Fe-NTA complex with the ferrozine reagent kit by a biochemical analyzer. To determine NTBI at extremely low concentrations, the program parameters for serum iron measurement were modified.

Results: Linearity was up to 15 μmol/L with analytical recovery of 93%–103%. The limit of detection was 0.076 μmol/L. The within-run coefficient of variation was 2.37%, 1.23%, and 0.812% at concentrations of 0.338, 1.717, and 5.916 μmol/L, respectively. NTBI concentrations measured after exercise in samples obtained from 14 rowers, divided into two groups, were substantially higher in all samples. The median NTBI concentrations (range) before and after exercise were 0.197 (–0.11 to 0.58), and 3.353 (2.39–8.97) μmol/L, respectively, in older rowers and 0.197 (–0.18 to 1.17), and 1.360 (0.47–2.49) μmol/L, respectively, in younger rowers.

Conclusions: With the described modification for serum iron determination, NTBI can be measured with high sensitivity and specificity. The data presented are illustrative examples of the applicability of this assay.
Clin Chem Lab Med 2010;48:1427–32.
Evaluation of D-dimer in the diagnosis of suspected aortic dissection
Authors: Fan Qing-kun , Wang Wen-wu , Zhang Zhen-lu , Liu Ze-jin , Yang Jun , Zhao Geng-sheng , Cao Shu-zheng 
Published: August 2010

Abstract

Background: The goal of this study was to evaluate plasma D-dimer as a diagnostic marker for exclusion of suspected aortic dissection (AD).

Methods: Two-hundred and sixty suspected AD patients were enrolled, including acute AD, n=107; chronic AD, n=17; acute myocardial infarction (AMI), n=70; pulmonary embolism (PE), n=18; non-ST elevation myocardial infarction (NSTEMI), n=28; and unstable angina (UA), n=20. All patients had D-dimer testing performed (Roche Diagnostics GmbH) immediately following admission.

Results: The D-dimer concentrations in both the acute AD group [median: 3.47; 95% confidence interval (CI): 2.43–4.50 μg/mL] and chronic AD group (median: 1.09; 95% CI: 0.36–3.81 μg/mL) were significantly higher than those in patients in the AMI, NSTEMI and UA groups (p=0.000), but not when compared to the PE group. One (0.8%) patient was identified in the acute AD group who presented with a low D-dimer value (0.04 μg/mL), indicating the existence of intramural hematoma as demonstrated by CT.

Conclusions: D-dimer may be used as a potential marker for suspected AD, with high sensitivity of up to 99.2% (1/124). Regardless of the cut-off threshold selected, the sensitivity of D-dimer was unable to reach 100%. Further examinations, including imaging technology, were necessary to diagnose the suspected AD patients who had negative D-dimer result.
Clin Chem Lab Med 2010;48:1733–7.
Carrier Transport in Homo- and Heteroepitaxial Zinc Oxide Layers
Authors: Ellmer Klaus 
Published: August 2010

AbstractHomo- and heteroepitaxial ZnMgO:Al, ZnCaO:Al and ZnO:Ga films have been grown on sapphire and ZnO substrates by RF (13.56 MHz) reactive magnetron sputtering from oxidic targets. The films grow epitaxially, i.e. with a preferred in-plane and out-of plane orientation. However, the heteroepitaxial films on sapphire exhibit a much higher crystallographic defect density, compared to the homepitaxial films. The ZnMeO films (Me – metal)on a-plane sapphire exhibit a lower defect density leading to higher Hall mobilities. Both, homo- and heteroepitaxial ZnO:Ga films with carrier concentrations N>1020 cm−3 exhibit the same mobility values, which increase with increasing carrier concentration. This behaviour is typical for electrical grain barrier limited transport, as decribed recently for polycrystalline ZnO:Al(Ga) films on glass. For the ZnCaO:Al films, deposited at similar conditions as the ZnO:Ga films, much lower carrier concentrations were measured, both for sapphire as well as for ZnO substrates. The mobilities of the ZnCaO:Al films on ZnO are much higher than that on the sapphire single crystals. The measured Hall mobilities are compared to single crystalline ZnO transport data.Additionally, the work functions of the ZnMeO layers have been measured by X-ray and ultra-violet photoelectron spectroscopy. As expected, the work functions are lower compared to unalloyed ZnO, which can be used for ZnO band gap and band alignment engineering.
Experimental Design for Free Space Nonlinear Magnetic Material Characterization Using Photonic Structures
Authors: Kuster Eric , Moore Ricky L. 
Published: August 2010

ABSTRACTMeasuring nonlinear AC dielectric or magnetic properties of ferro and ferri magnetic materials has often required large, extremely high power and bulky equipment configurations for production of the required intense electric and/or magnetic fields. Multiple RF cavities, striplines or waveguide test fixtures may be required. The techniques often require 10s of cubic millimeter too centimeter material volumes. This paper presents results from an initial experimental design of a free space based measurement configuration for small material volumes such as nano and micro particulates or particulate composites. The technique uses wideband radiators and modest variable power radio frequency pumping sources. A second design uses, in concert with a higher power pump, a variable frequency low power probe source at frequencies other than that of the pump. A two dimensional photonic bandgap (PBG) structure is common to both configurations. The photonic structure acts to enhance power density at frequencies associated with localized electromagnetic fields constrained to small volumes of the photonic structures. Field localization is recognized and has been applied in biological diagnostics and treatment [Phys. Rev. v109, 1492; Phys. Rev. B, v55 and 62, n. 19 and 16, pp 13234 and 11230 and Chem.Soc.News, 1998, v27, p241].Modeling of various measurement configurations is based upon expansion of incident and propagating fields in characteristic modes external and within the structure. A proper choice of photonic structure, material and pump frequency is found to localize fields in air, between the structural dielectric members of the photonic structure. This will allow small magnetic or electric samples to be inserted for exposure in these regions. The electromagnetic reflection, transmission, absorption and field/power density multiplier of the photonic structure can be measured at multiple frequencies and reflect the dielectric or magnetic nonlinearity and changed dispersion induced at the pump frequency. One PBG-free space combination will be presented that finds power density multipliers of 10 6. Thus a 10 watt pump source will produce RF magnetic field strengths near 10 Oe. This magnetic field should be sufficient to exceed critical fields for many ferri and ferromagnetic samples inserted in the volume of field localization.
Mechanosynthesis, Radiation-Thermal Modification and Characterization of Nanostructured Scandia Stabilized Zirconia Ceramics
Authors: Zyryanov Vladimir V. , Uvarov Nikolay F. , Ulihin Artem S. , Sadykov Vladislav A. 
Published: August 2010

AbstractSSZ-based ceramics were obtained by sintering of nanopowders derived at room temperature by mechanochemical synthesis from refined technical grade ZrO2 nano-precursors. RT-treatment by 2.5 MeV electrons up to 1563 K was used for the modification of ceramics. Powders and ceramics were characterized by XRD, Raman, SEM and EDS, TEM, SIMS techniques. The phase composition of Zr0.89Sc0.1Ce0.01O1.95 ceramics was very close to cubic structure but better fitting of XRD patterns was obtained for rhombohedral lattice. Conductivity of solid electrolytes for IT SOFC was studied by complex impedance method. To stabilize cubic structure and increase conductivity at operation temperature of To ∼ 1000 K, the composition of SSZ solid electrolyte was optimized by addition of yttria and sintering aids. The interaction of admixtures with minor dopants leading to intergrain phase was revealed. During fast sintering, ceramics keep a memory about inhomogeneous disordered solid solutions in a form of nanostructuring. Conductivity data indicate nanostructuring of ceramics too: activation energies of bulk and grain boundary conductivities are close (Eb ∼ 0.9 eV, Egb ∼ 1.05 eV). Annealing of ceramics at high temperatures increases conductivity at To and promotes grain growth.
On the Characterisatiopn of Order-Disorder in Ion-Irradiated Pyrochlore Compounds by Electron Scattering Methods
Authors: Lumpkin Gregory R. , Whittle Karl R. , Blackford Mark G. , Smith Katherine L. , Zaluzec Nestor J. 
Published: August 2010

AbstractSelected area electron diffraction patterns are routinely used to determine the effects of irradiation damage in nuclear materials. Using zone axis orientations, the intensities of Bragg beams change from a dynamical to kinematic-like state due to the presence of amorphous domains in the material. Such changes in beam intensities, together with the increased diffuse scattering from the increasing amorphous fraction, present a major obstacle to the determination of cation or anion disorder in the crystalline fraction.