bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assaying pharmacodynamic endpoints with targeted therapy: Flavopiridol and 17AAG induced dephosphorylation of histone H1.5 in acute myeloid leukemia
Authors: Wang Liwen , Harshman Sean W. , Liu Shujun , Ren Chen , Xu Hua , Sallans Larry , Grever Michael , Byrd John C. , Marcucci Guido , Freitas Michael A. 
Published: October 2010

AbstractHistone H1 is commonly used to assay kinase activity in vitro. As many promising targeted therapies affect kinase activity of specific enzymes involved in cancer transformation, H1 phosphorylation can serve as potential pharmacodynamic marker for drug activity within the cell. In this study we utilized a phosphoproteomic workflow to characterize histone H1 phosphorylation changes associated with two targeted therapies in the Kasumi‐1 acute myeloid leukemia cell line. The phosphoproteomic workflow was first validated with standard casein phosphoproteins and then applied to the direct analysis of histone H1 from Kasumi‐1 nuclear lysates. Ten H1 phosphorylation sites were identified on the H1 variants, H1.2, H1.3, H1.4, H1.5 and H1.x. LC MS profiling of intact H1s demonstrated global dephosphorylation of H1.5 associated with therapy by the cyclin‐dependent kinase inhibitor, flavopiridol and the Heat Shock Protein 90 inhibitor, 17‐(Allylamino)‐17‐demethoxygeldanamycin. In contrast, independent treatments with a nucleotide analog, proteosome inhibitor and histone deacetylase inhibitor did not exhibit decreased H1.5 phosphorylation. The data presented herein demonstrate that potential of histones to assess the cellular response of reagents that have direct and indirect effects on kinase activity that alters histone phosphorylation. As such, this approach may be a highly informative marker for response to targeted therapies influencing histone phosphorylation.
Protein abundances are more conserved than mRNA abundances across diverse taxa
Authors: Laurent Jon M. , Vogel Christine , Kwon Taejoon , Craig Stephanie A. , Boutz Daniel R. , Huse Holly K. , Nozue Kazunari , Walia Harkamal , Whiteley Marvin , Ronald Pamela C. , Marcotte Edward M. 
Published: October 2010

AbstractProteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post‐transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large‐scale protein and mRNA expression data sets from seven different species: two bacteria, yeast, nematode, fly, human, and rice. We find that steady‐state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge.
Synthesis, structure, and optical properties of an alternating calix[4]arene‐based meta‐linked phenylene ethynylene copolymer
Authors: Barata Patrícia D. , Costa Alexandra I. , Ferreira Luís F. V. , Prata José V. 
Published: October 2010

AbstractNovel alternating copolymers comprising bis‐ calix[4]arene‐p‐phenylene ethynylene and m‐phenylene ethynylene units (CALIX‐m‐PPE) were synthesized using the Sonogashira‐Hagihara cross‐coupling polymerization. Good isolated yields (60–80%) were achieved for the polymers that show Mn ranging from 1.4 × 104 to 5.1 × 104 gmol−1 (gel permeation chromatography analysis), depending on specific polymerization conditions. The structural analysis of CALIX‐m‐PPE was performed by 1H, 13C, 13C–1H heteronuclear single quantum correlation (HSQC), 13C–1H heteronuclear multiple bond correlation (HMBC), correlation spectroscopy (COSY), and nuclear overhauser effect spectroscopy (NOESY) in addition to Fourier transform‐Infrared spectroscopy and microanalysis allowing its full characterization. Depending on the reaction setup, variable amounts (16–45%) of diyne units were found in polymers although their photophysical properties are essentially the same. It is demonstrated that CALIX‐m‐PPE does not form ground‐ or excited‐state interchain interactions owing to the highly crowded environment of the main‐chain imparted by both calix[4]arene side units which behave as insulators inhibiting main‐chain π–π staking. It was also found that the luminescent properties of CALIX‐m‐PPE are markedly different from those of an all‐p‐linked phenylene ethynylene copolymer (CALIX‐p‐PPE) previously reported. The unexpected appearance of a low‐energy emission band at 426 nm, in addition to the locally excited‐state emission (365 nm), together with a quite low fluorescence quantum yield (ϕ = 0.02) and a double‐exponential decay dynamics led to the formulation of an intramolecular exciplex as the new emissive species. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Synthesis of 4μ‐PS2PEO2, 4μ‐PS2PCL2, 4μ‐PI2PEO2, and 4μ‐PI2PCL2 star‐shaped copolymers by the combination of glaser coupling with living anionic polymerization and ring‐opening polymerization
Authors: Wang Guowei , Fan Xiaoshan , Huang Junlian 
Published: October 2010

Abstract4μ‐A2B2 star‐shaped copolymers contained polystyrene (PS), poly(isoprene) (PI), poly(ethylene oxide) (PEO) or poly(ε‐caprolactone) (PCL) arms were synthesized by a combination of Glaser coupling with living anionic polymerization (LAP) and ring‐opening polymerization (ROP). Firstly, the functionalized PS or PI with an alkyne group and a protected hydroxyl group at the same end were synthesized by LAP and then modified by propargyl bromide. Subsequently, the macro‐initiator PS or PI with two active hydroxyl groups at the junction point were synthesized by Glaser coupling in the presence of pyridine/CuBr/N,N,N ′,N ″,N ″‐penta‐methyl diethylenetri‐amine (PMDETA) system and followed by hydrolysis of protected hydroxyl groups. Finally, the ROP of EO and ε‐CL monomers was carried out using diphenylmethyl potassium (DPMK) and tin(II)‐bis(2‐ethylhexanoate) (Sn(Oct)2) as catalyst for target star‐shaped copolymers, respectively. These copolymers and their intermediates were well characterized by SEC, 1H NMR, MALDI‐TOF mass spectra and FT‐IR in details. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Stimuli‐responsive polymer hydrogels containing partially exfoliated graphite
Authors: Alzari Valeria , Mariani Alberto , Monticelli Orietta , Valentini Luca , Nuvoli Daniele , Piccinini Massimo , Scognamillo Sergio , Bon Silvia Bittolo , Illescas Javier 
Published: October 2010

AbstractIn this work, a new stimuli‐responsive composite polymer hydrogel containing partially exfoliated graphite was prepared by frontal polymerization. The materials obtained were characterized by differential scanning calorimetry, RAMAN, scan electron microscopy, transmission electron microscopy, atomic force microscopy, and in terms of swelling behavior. It was found that the maximum temperature reached by the polymerization front and the lower critical solution temperature are affected by the graphite content. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Preparation of homogeneous titania coatings on the surface of MWNTs
Authors: Németh Zoltán , Réti Balázs , Dieker Christel , Kukovecz Ákos , Alexander Duncan T. L. , Seo Jin Won , Forró László , Hernadi Klara 
Published: October 2010

AbstractThe aim of this work was to develop a controllable route to produce a stable and inorganic layer on the surface of multi‐wall carbon nanotubes. Precursor compounds such as TiBr4, TiCl4, Ti(OiPr)4, and Ti(OEt)4 were used to cover the surface of carbon nanotubes (CNTs) under either solvent free or solution conditions. Various titania precursors were compared in the formation of homogeneous layers on the surface of CNTs. As‐prepared titania coverages were characterized by transmission electron microscopy (TEM), high resolution TEM, scanning electron microscopy, electron energy loss spectroscopy, and X‐ray diffraction techniques. Results revealed that homogeneous coverage can be achieved in a controllable way.
Indium incorporation in GaInN/GaN quantum well structures on polar and nonpolar surfaces
Authors: Jönen Holger , Rossow Uwe , Bremers Heiko , Hoffmann Lars , Brendel Moritz , Dräger Alexander Daniel , Metzner Sebastian , Bertram Frank , Christen Jürgen , Schwaiger Stephan , Scholz Ferdinand , Thalmair Johannes , Zweck Josef , Hangleiter Andreas 
Published: October 2010

AbstractGaInN/GaN multiple quantum well structures grown on polar and nonpolar surfaces have been compared with respect to the indium incorporation efficiency in the quantum wells (QWs). Under the same growth conditions X‐ray diffraction measurements reveal similar growth rates and In concentrations for c‐plane, a‐plane, and m‐plane with In contents up to 40%. These results are in good agreement with optical experiments, in particular for homoepitaxial growth. However, there is strong evidence that the optical properties of the nonpolar heteroepitaxial GaInN QWs are dominated by the high density of stacking faults in those samples.
Comparison of secondary ion mass spectrometry and micromilling/continuous flow isotope ratio mass spectrometry techniques used to acquire intra‐otolith δ18O values of wild Atlantic salmon (Salmo salar)
Authors: Hanson N. N. , Wurster C. M. , EIMF  , Todd C. D. 
Published: October 2010

AbstractThe chemical signals in the sequential layers of fish otoliths have the potential to provide fisheries biologists with temporal and spatial details of migration which are difficult to obtain without expensive tracking methods. Signal resolution depends, however, on the extraction technique used. We compared the use of mechanical micromilling and continuous flow isotope ratio mass spectrometry (CF‐IRMS) methods with secondary ion mass spectrometry (SIMS) to obtain δ18O profiles from otoliths of wild Atlantic salmon (Salmo salar) and used these to corroborate the time of freshwater emigration of the juvenile with macroscopic patterns within the otolith. Both techniques showed the transition occurring at the same visible feature on the otolith, allowing future analyses to easily identify the juvenile (freshwater) versus adult (marine) life‐stages. However, SIMS showed a rapid and abrupt transition whereas micromilling provided a less distinct signal. The number of samples that could be obtained per unit area sampled using SIMS was 2 to 3 times greater than that when using micromilling/CF‐IRMS although the δ18O values and analytical precisions (∼0.2‰) of the two methods were comparable. In addition, SIMS δ18O results were used to compare otolith aragonite values with predicted values calculated using various isotope fractionation equations. Copyright © 2010 John Wiley & Sons, Ltd.
Nanostructured bladder tissue replacements
Authors: Chun Young Wook , Lim Hojean , Webster Thomas J. , Haberstroh Karen M. 
Published: October 2010

AbstractThe interaction between cells or tissues and natural or synthetic materials which mimic the natural biological environment has been a matter of great interest in tissue engineering. In particular, surface properties of biomaterials (regardless of whether they are natural or synthetic) have been optimized using nanotechnology to improve interactions with cells for regenerative medicine applications. Specifically, in vivo and in vitro studies have demonstrated greater bladder tissue growth on polymeric surfaces with nanoscale to submicron surface features. Improved bladder cell responses on nanostructured polymers have been correlated to unique nanomaterial surface features leading to greater surface energy which influences initial protein interactions. Moreover, coupled with the observed greater in vitro and in vivo bladder cell adhesion as well as proliferation on nanostructured compared to conventional synthetic polymers, decreased calcium stone formation has also been measured. In this article, the importance of nanostructured biomaterial surface features for bladder tissue replacements are reviewed with thoughts on future directions for this emerging field. WIREs Nanomed Nanobiotechnol 2011 3 134–145 DOI: 10.1002/wnan.89This article is categorized under:

Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement
Formation of Nanopits in Si Capping Layers on SiGe Quantum Dots
Authors: Cui Jian , Lin Jian Hui , Wu Yue Qin , Fan Yong Liang , Zhong Zhenyang , Yang Xin Ju , Jiang Zui Min 
Published: October 2010

Abstract
In-situ annealing at a high temperature of 640°C was performed for a low temperature grown Si capping layer, which was grown at 300°C on SiGe self-assembled quantum dots with a thickness of 50 nm. Square nanopits, with a depth of about 8 nm and boundaries along 〈110〉, are formed in the Si capping layer after annealing. Cross-sectional transmission electron microscopy observation shows that each nanopit is located right over one dot with one to one correspondence. The detailed migration of Si atoms for the nanopit formation is revealed by in-situ annealing at a low temperature of 540°C. The final well-defined profiles of the nanopits indicate that both strain energy and surface energy play roles during the nanopit formation, and the nanopits are stable at 640°C. A subsequent growth of Ge on the nanopit-patterned surface results in the formation of SiGe quantum dot molecules around the nanopits.
Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents
Authors: Gill Navdeep , SanMiguel Phillip , Dhillon Braham Deep Singh , Abernathy Brian , Kim HyeRan , Stein Lincoln , Ware Doreen , Wing Rod , Jackson Scott A. 
Published: October 2010

Abstract
Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives.
Utilization of IκB–EGFP Chimeric Gene as an Indicator to Identify Microbial Metabolites with NF-κB Inhibitor Activity
Authors: Lin Yu-Ling , Chen Yen-Shun , Hsieh Jui-Hung , Lin Ching-Min , Wu Hsin-Yi , Lin Chen-Si , Chu Rea-Min , Liao Kuang-Wen , Hsu Yuan-Hsun 
Published: October 2010

Abstract
NF-κB regulates several important expressions, such as cytokine release, anti-apoptosis, adhesion molecule expression, and cell cycle processing. Several NF-κB inhibitors have been discovered as an anti-tumor or anti-inflammatory drug. The activity of NF-κB transcription factor is negatively regulated by IκB binding. In this study, IκB assay system was established and IκB–EGFP fusion protein was used as an indicator to monitor the effects of substances on the IκB degradation. The results indicated that the chosen hydroquinone could inhibit the IκB degradation and cause the cell de-attachment from the bottom of culture plate. In addition, this system could also monitor the IκB degradation of microbial metabolite of natural mixtures of propolis. Thus, the IκB assay system may be a good system for drug discovery related to microbial metabolite.
Imaging for suspected pulmonary embolism in pregnancy—what about the fetal dose? A comprehensive review of the literature
Authors: Niemann Tilo , Nicolas Guillaume , Roser Hans W. , Müller-Brand Jan , Bongartz Georg 
Published: October 2010

Abstract

Objective
To give a comprehensive overview of fetal doses reported in the literature when imaging the pregnant woman with suspected pulmonary embolism (PE).

Methods
A comprehensive literature search in the PubMed, MEDLINE and EMBASE databases yielded a total of 1,687 papers that were included in the analysis and have been analysed with regard to fetal dose in suspected PE radiological imaging strategies.

Results
Fetal dose in chest computed tomography (CT) ranges between 0.013 and 0.026 mGy in early and 0.06–0.1 mGy in late pregnancy compared with 99mTc-MAA perfusion scintigraphy with a fetal dose of 0.1–0.6 mGy in early and 0.6–0.8 mGy in late pregnancy. 99mTc-aerosol ventilation scintigraphy results in 0.1–0.3 mGy. However, there is concern about female breast irradiation in CT, which is higher than in scintigraphy. CT radiation risks for breast tissue remain unclear.

Conclusion
Knowledge of dosimetry and radiation risks is crucial in the radiological work-up of suspected PE in pregnancy. It is reasonable to reserve scintigraphy for pregnant patients with normal chest radiography findings and no history of asthma or chronic lung disease. Performing CT applying dose reduction instead of scintigraphy will minimise fetal radiation dose and maximise the diagnostic value.
The role of depression and catastrophizing in musculoskeletal pain
Authors: Lintonl Steven J. , Nicholasl Michael K. , MacDonaldl Shane , Boersmal Katja , Bergboml Sofia , Maherl Chris , Refshaugel Kathy 
Published: October 2010

AbstractMany patients with musculoskeletal pain also suffer from a depressed mood. Catastrophizing is one process that may link depression and pain since it is a key concept in models of both problems. Earlier research has suggested that catastrophizing measures something above and beyond depression. This study tests the idea that if depressed mood and catastrophizing are separate entities then when one is absent the other should still contribute to poor outcome, and, when both are present there should be an additional adverse effect.To this end, a prospective design, with a built‐in replication from two clinical samples of patients with sub‐acute pain (one from Sweden, N=373; one from Australasia, N=259), was employed. Participants were classified as to having high/low scores on measures of depression and catastrophizing. Subsequently, these classifications were studied in relation to outcome variables cross‐sectionally and at follow‐up.Results showed a small to moderate correlation between catastrophizing and depression and that there are individuals with one, but not the other problem. Further, having one or the other of the entities was associated with current pain problems and outcome, while having both increased the associations substantially. The replication showed very similar resultsOur data demonstrate that pain catastrophizing and heightened depressed mood have an additive and adverse effect on the impact of pain, relative to either alone. It suggests that each should be assessed in the clinic and that future research should focus on treatments specifically designed to tackle both depressed mood and catastrophizing.
Circulating smallpox knowledge: Guatemalan doctors, Maya Indians and designing Spain's smallpox vaccination expedition, 1780–1803
Authors: FEW MARTHA 
Published: October 2010

AbstractDrawing on the rich but mostly overlooked history of Guatemala's anti-smallpox campaigns in the 1780s and 1790s, this paper interweaves an analysis of the contribution of colonial medical knowledges and practical experiences with the construction and implementation of imperial science. The history of the anti-smallpox campaigns is traced from the introduction of inoculation in Guatemala in 1780 to the eve of the Spanish Crown-sponsored Royal Maritime Vaccination Expedition in 1803. The paper first analyses the development of what Guatemalan medical physician José Flores called his ‘local method’ of inoculation, tailored to material and cultural conditions of highland Maya communities, and based on his more than twenty years of experience in anti-smallpox campaigns among multiethnic populations in Guatemala. Then the paper probes the accompanying transformations in discourses about health through the anti-smallpox campaigns as they became explicitly linked to new discourses of moral responsibility towards indigenous peoples. With the launch of the Spanish Vaccination Expedition in 1803, anti-smallpox efforts bridged the New World, Europe and Asia, and circulated on a global scale via the enactment of imperial Spanish health policy informed, in no small part, by New World and specifically colonial Guatemalan experiences with inoculation in multiethnic cities and highland Maya towns.
Occurrence of four additional non-hairy species ofLeptogiumfrom Maharashtra, India
Authors: DUBE Archana , MAKHIJA Urmila 
Published: October 2010

AbstractIn the present paper four etomentose species ofLeptogiumare recorded from Maharashtra, western India. Three species, viz.Leptogium patwardhaniiDube & Makhija sp. nov., Leptogium subazureumDube & Makhija sp. nov., andLeptogium verrucosumDube & Makhija sp. nov., are described as new to science and one species,Leptogium propaguliferumVain., is recorded for the first time from India. A revised key to the non-hairy species ofLeptogiumfrom India is provided.
New data forRinodina flavosoralifera
Authors: GIRALT Mireia , van den BOOM Pieter P. G. , TØNSBERG Tor , ELIX John A. 
Published: October 2010

AbstractWell-developed ascospores ofRinodina flavosoraliferahave been observed for the first time. The ascospores are described and illustrated and new data on the chemistry and distribution of this species are provided. New chorological data onRinodina disjunctaare also included.
Lecanora antiqua, a new saxicolous species from Great Britain, and the nomenclature and authorship of L. albescens, L. conferta and L. muralis
Authors: LAUNDON Jack Rodney 
Published: October 2010

AbstractLecanora albescens (Hoffm.) Branth & Rostr. is the correct authorship of this species, and the combination cannot be attributed to Flörke. Lecanora antiqua J. R. Laundon is described for the lichen previously, but wrongly, known in Britain as L. conferta; it is remarkable in occupying the interface between acid and calcareous surfaces on the vertical walls of medieval churches. The nomenclature of the lobed Lecanora, which has had two alternative Latin names since the early 19th century, namely L. muralis Rabenh. and L. saxicola (Pollich) Ach., has been studied and the latter was found to be correct.
A new species of Leiorreuma Eschw. from India
Authors: DUBEY Urvashi , UPRETI Dalip K. , NAYAKA Sanjeeva 
Published: October 2010

AbstractLeiorreuma subpatellulum is described as new to science. The new species has a completely carbonized exciple, an inspersed hymenium and brown ascospores with 6–12 locules, tapering at one end.