bluuebunny/crossref_metadata_2025 huggingface dataset:
Mini-Workshop: The Homotopy Interpretation of Constructive Type Theory
Authors: Awodey Steve , Garner Richard , Martin-Löf Per , Voevodsky Vladimir
Published: September 2011

Over the past few years it has become apparent that there is a surprising and deep connection between constructive logic and higherdimensional structures in algebraic topology and category theory, in the form of an interpretation of the dependent type theory of Per Martin-Löf into classical homotopy theory. The interpretation results in a bridge between the worlds of constructive and classical mathematics which promises to shed new light on both. This mini-workshop brought together researchers in logic, topology, and cognate fields in order to explore both theoretical and practical ramifications of this discovery.
A statistical and event study of magnetotail dipolarization fronts
Authors: Schmid D. , Volwerk M. , Nakamura R. , Baumjohann W. , Heyn M.
Published: September 2011

Abstract. A study of dipolarization fronts of the Earth's magnetotail has been performed using seven years (2001–2007) of Cluster data. Events both with and without high-speed earthward flows are included. A superposed epoch analysis of the data shows that the dipolarization is preceeded by a decrease of Bz before the increase. The duration of the dipolarization tends to be decreasing with increasing velocity of the plasma flows. The thickness of the dipolarization front is on average 1.8 plasma inertial lengths, independent of the plasma velocity. We find that the events fall into two categories: Earthward and tailward moving dipolarizations. The dipolarization fronts can be assumed to be tangential discontinuities and the currents on the front have mainly a perpendicular component.
Interplanetary magnetic field rotations followed from L1 to the ground: the response of the Earth's magnetosphere as seen by multi-spacecraft and ground-based observations
Authors: Volwerk M. , Berchem J. , Bogdanova Y. V. , Constantinescu O. D. , Dunlop M. W. , Eastwood J. P. , Escoubet P. , Fazakerley A. N. , Frey H. , Hasegawa H. , Lavraud B. , Panov E. V. , Shen C. , Shi J. K. , Taylor M. G. G. T. , Wang J. , Wild J. A. , Zhang Q. H. , Amm O. , Weygand J. M.
Published: September 2011

Abstract. A study of the interaction of solar wind magnetic field rotations with the Earth's magnetosphere is performed. For this event there is, for the first time, a full coverage over the dayside magnetosphere with multiple (multi)spacecraft missions from dawn to dusk, combined with ground magnetometers, radar and an auroral camera, this gives a unique coverage of the response of the Earth's magnetosphere. After a long period of southward IMF Bz and high dynamic pressure of the solar wind, the Earth's magnetosphere is eroded and compressed and reacts quickly to the turning of the magnetic field. We use data from the solar wind monitors ACE and Wind and from magnetospheric missions Cluster, THEMIS, DoubleStar and Geotail to investigate the behaviour of the magnetic rotations as they move through the bow shock and magnetosheath. The response of the magnetosphere is investigated through ground magnetometers and auroral keograms. It is found that the solar wind magnetic field drapes over the magnetopause, while still co-moving with the plasma flow at the flanks. The magnetopause reacts quickly to IMF Bz changes, setting up field aligned currents, poleward moving aurorae and strong ionospheric convection. Timing of the structures between the solar wind, magnetosheath and the ground shows that the advection time of the structures, using the solar wind velocity, correlates well with the timing differences between the spacecraft. The reaction time of the magnetopause and the ionospheric current systems to changes in the magnetosheath Bz seem to be almost immediate, allowing for the advection of the structure measured by the spacecraft closest to the magnetopause.
Vegetation-climate interactions in the warm mid-Cretaceous
Authors: Zhou J. , Poulsen C. J. , Rosenbloom N. , Shields C. , Briegleb B.
Published: September 2011

Abstract. Vegetation-climate interactions are thought to have amplified polar warmth during past warm periods. Here, we explore the vegetation-climate interactions in the mid- Cretaceous using a fully coupled ocean-atmosphere general circulation model with a dynamic vegetation component. We run simulations with 1×, 10× and 16× preindustrial atmospheric CO2. Results show that forests expand from mid-latitudes to high latitudes as CO2 increases from 1× to 10× and 16×, mainly due to the CO2- induced warming. This expansion of mid-to-high latitude forests are largely supported by the distribution of mid-Cretaceous fossil woods and coal deposits. Globally, the presence of vegetation increases mean annual temperature and precipitation by 0.9 °C and 0.11mm day−1 relative to bare ground. High-latitude warming induced by the presence of vegetation (∼1.9 °C) is less than half of that reported in previous studies. The weaker warming here is mainly due to less pronounced albedo feedbacks, and to a less extent, reduced poleward heat transport via weakening of the meridional overturning circulation. Our results suggest that other mechanisms in addition to high atmospheric CO2 and high-latitude vegetation are required to maintain the polar warmth.
Assimilation of Earth rotation parameters into a global ocean model: excitation of polar motion
Authors: Saynisch J. , Wenzel M. , Schröter J.
Published: September 2011

Abstract. The oceanic contribution to Earth rotation anomalies can be manifold. Possible causes are a change of total ocean mass, changes in current speed or location and changes in mass distribution. To derive the governing physical mechanisms of oceanic Earth rotation excitation we assimilate Earth rotation observations with a global circulation ocean model. Before assimilation, observations of length of day and polar motion were transformed into estimates of ocean angular momentum. By using the adjoint 4D-VAR assimilation method we were able to reproduce these estimated time series. Although length of day was assimilated simultaneously the analysis in this paper focuses on the oceanic polar motion generation. Our results show that changes in mass distribution and currents contribute to oceanic polar motion generation. Both contributions are highly correlated and show similar amplitudes. The changes in the model done by the assimilation procedure could be related to changes in the atmospheric forcing. Since for geometrical reasons the change of total ocean mass does not project on polar motion, we conclude that the polar motion is mainly generated by a geostrophic response to atmospheric momentum forcing. In geostrophic currents mass displacement and current speed entail each other. This way the large similarity of mass and current generated ocean angular momentum can be explained.
Towards a regional ocean forecasting system for the IBI (Iberia-Biscay-Ireland area): developments and improvements within the ECOOP project framework
Authors: Cailleau S. , Chanut J. , Lellouche J.-M. , Levier B. , Maraldi C. , Reffray G. , Garcia Sotillo M.
Published: September 2011

Abstract. ECOOP project allowed the improvement of the regional and coastal operational forecasting systems for the different European Seas. In the Iberia-Biscay-Ireland area (IBI) a regional system has been developed and improved for the project in order to provide IBI partners the best initial and boundary conditions to their embedded coastal systems. End users could also get access to the regional hindcasts and forecasts through the ECOOP website. This system has been upgraded as follow: a first existing version V0, a second base-line version V1 ready for the ECOOP Target Operational Period and a third one V2 which consists in a new generation regional system. This paper especially pays attention to the improvements from the V1 system, whose physics are close to a large scale basin system, to the V2 one which physics are more adapted to shelf and coastal issues. Strong developments which allow further regional physics resolution in the NEMO OGCM such as tide, non linear free surface and adapted vertical mixing scheme among other have been carried out from V1 to V2 versions for the project. Thus, regional thermal fronts due to tidal mixing appear in V2 solution and are quite well placed. Moreover, simulation of the stratification in shelf areas is also improved in V2.
Development of a Website and Biobank Database for the Nanosized Cancer Polymarker Biochip Project: A Multicenter Italian Experience
Authors: Leon Antonette E. , Fabricio Aline S.C. , Benvegnù Fabio , Michilin Silvia , Secco Annamaria , Spangaro Omar , Meo Sabrina , Gion Massimo
Published: September 2011

The Nanosized Cancer Polymarker Biochip Project (RBLA03S4SP) funded by an Italian MIUR-FIRB grant (Italian Ministry of University and Research - Investment Funds for Basic Research) has led to the creation of a free-access dynamic website, available at the web address https://serviziweb.ulss12.ve.it/firbabo , and of a centralized database with password-restricted access. The project network is composed of 9 research units (RUs) and has been active since 2005. The aim of the FIRB project was the design, production and validation of optoelectronic and chemoelectronic biosensors for the simultaneous detection of a novel class of cancer biomarkers associated with immunoglobulins of the M class (IgM) for early diagnosis of cancer. Biomarker immune complexes (BM-ICs) were assessed on samples of clinical cases and matched controls for breast, colorectal, liver, ovarian and prostate malignancies.

This article describes in detail the architecture of the project website, the central database application, and the biobank developed for the FIRB Nanosized Cancer Polymarker Biochip Project. The article also illustrates many unique aspects that should be considered when developing a database within a multidisciplinary scenario.

The main deliverables of the project were numerous, including the development of an online database which archived 1400 case report forms (700 cases and 700 matched controls) and more than 2700 experimental results relative to the BM-ICs assayed. The database also allowed for the traceability and retrieval of 21,000 aliquots archived in the centralized bank and stored as backup in the RUs, and for the development of a centralized biological bank in the coordinating unit with 6300 aliquots of serum.

The constitution of the website and biobank database enabled optimal coordination of the RUs involved, highlighting the importance of sharing samples and scientific data in a multicenter setting for the achievement of the project goals.
RNA Aptamers and Spiegelmers: Synthesis, Purification, and Post‐Synthetic PEG Conjugation
Authors: Hoffmann Stefanie , Hoos Johannes , Klussmann Sven , Vonhoff Stefan
Published: September 2011

This unit describes the solid‐phase synthesis and downstream processing for RNA oligonucleotides with a length of up to 40 to 50 nucleotides on a 1‐ to 4‐mmol scale with subsequent conjugation to PEG using the L‐RNA spiegelmer NOX‐E36 as an example. Following synthesis and two‐step deprotection, the crude oligonucleotide is purified by preparative reversed‐phase HPLC and desalted by tangential flow ultrafiltration. The resulting intermediate amino‐modified oligonucleotide is reacted with NHS‐ester‐activated PEG, and the oligonucleotide‐PEG conjugate is obtained after preparative AX‐HPLC purification, followed by ultrafiltration and lyophilization. Critical process parameters are described, as well as time considerations and examples for analytical methods used as in‐process and quality controls. Curr. Protoc. Nucleic Acid Chem. 46:4.46.1‐4.46.30. © 2011 by John Wiley & Sons, Inc.
Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups
Authors: Fischer Steve , Brunk Brian P. , Chen Feng , Gao Xin , Harb Omar S. , Iodice John B. , Shanmugam Dhanasekaran , Roos David S. , Stoeckert Christian J.
Published: September 2011

OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL‐DB is a public database that allows users to browse and view ortholog groups that were pre‐computed using the OrthoMCL algorithm. Version 4 of this database contained 116,536 ortholog groups clustered from 1,270,853 proteins obtained from 88 eukaryotic genomes, 16 archaean genomes, and 34 bacterial genomes. Future versions of OrthoMCL‐DB will include more proteomes as more genomes are sequenced. Here, we describe how you can group your proteins of interest into ortholog clusters using two different means provided by the OrthoMCL system. The OrthoMCL‐DB Web site has a tool for uploading and grouping a set of protein sequences, typically representing a proteome. This method maps the uploaded proteins to existing groups in OrthoMCL‐DB. Alternatively, if you have proteins from a set of genomes that need to be grouped, you can download, install, and run the stand‐alone OrthoMCL software. Curr. Protoc. Bioinform. 35:6.12.1‐6.12.19. © 2011 by John Wiley & Sons, Inc.
Biological Sequence Motif Discovery Using motif‐x
Authors: Chou Michael F. , Schwartz Daniel
Published: September 2011

The Web‐based motif‐x program provides a simple interface to extract statistically significant motifs from large data sets, such as MS/MS post‐translational modification data and groups of proteins that share a common biological function. Users upload data files and download results using common Web browsers on essentially any Web‐compatible computer. Once submitted, data analyses are performed rapidly on an associated high‐speed computer cluster and they produce both syntactic and image‐based motif results and statistics. The protocols presented demonstrate the use of motif‐x in three common user scenarios. Curr. Protoc. Bioinform. 35:13.15.1‐13.15.24. © 2011 by John Wiley & Sons, Inc.
A Thermoresponsive Antimicrobial Wound Dressing Hydrogel Based on a Cationic Betaine Ester
Authors: Mi Luo , Xue Hong , Li Yuting , Jiang Shaoyi
Published: September 2011

This work reports a thermoresponsive multifunctional wound dressing hydrogel based on ABA triblock copolymers synthesized via reversible addition fragmentation chain transfer (RAFT) polymerization. The inner B block consists of a positively‐charged hydrolysable betaine ester loaded with an antimicrobial drug as its counter ion and the B block is flanked by two outer A blocks of thermoresponsive poly (N‐isopropylacrylamide) (PNIPAM). A solution containing the triblock copolymers can be applied to wound sites and immediately turns into a physical gel at the body temperature. This wound dressing can reduce the risk of wound infection by releasing small‐molecular‐weight antimicrobial drug and facilitate the attachment of mammalian cells during tissue regeneration through its positive surface charge. The cationic betaine ester can then hydrolyze at the wound site to its zwitterionic form, which is known to be biocompatible and nonsticky. The thermoresponsive in situ gelation feature along with controlled drug release, enhanced tissue–hydrogel interactions as well as long‐term biocompatibility make this hydrogel a very promising material for antimicrobial wound dressing applications.
Chalcopyrite Semiconductors for Quantum Well Solar Cells
Authors: Afshar Maziar , Sadewasser Sascha , Albert Jürgen , Lehmann Sebastian , Abou‐Ras Daniel , Marrón David Fuertes , Rockett Angus A. , Räsänen Esa , Lux‐Steiner Martha Ch.
Published: September 2011

The possibilities of using highly absorbing chalcopyrite semiconductors of the type Cu(In,Ga)Se2 in a quantum well solar cell structure are explored. Thin alternating layers of 50 nm CuInSe2 and CuGaSe2 were grown epitaxially on a GaAs(100) substrate. The optical properties of a resulting structure of three layers indicate charge carrier confinement in the low band gap CuInSe2 layer. By compositional analysis interdiffusion of In and Ga at the interfaces was found. The compositional profile was converted into a conduction‐band diagram, for which the quantization of energy levels was numerically confirmed using the effective‐mass approximation. The results provide a promising basis for the future development of chalcopyrite‐type quantum well structures and their application, i.e. in quantum well solar cells.
Vitamin D insufficiency in myeloproliferative neoplasms and myelodysplastic syndromes: Clinical correlates and prognostic studies
Authors: Pardanani Animesh , Drake Matthew T. , Finke Christy , Lasho Terra L. , Rozell Shaina A. , Jimma Thitina , Tefferi Ayalew
Published: September 2011

Vitamin D insufficiency is commonly observed in the general population; observational studies have suggested an association with increased risk of cancer development. We examined the clinical and prognostic relevance of low plasma levels of 25‐hydroxyvitamin D (25[OH]D) in myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS). A total of 409 patients were studied: 247 (60%) with primary myelofibrosis (PMF), 74 (18%) with de novo MDS, 63 (15%) with polycythemia vera (PV), and 25 (6%) with essential thrombocythemia (ET). Plasma 25(OH)D levels were measured by liquid chromatography‐tandem mass spectrometry; a level lower than 25 ng/mL indicated vitamin D insufficiency and a level lower than 10 ng/mL indicated severe deficiency. The proportion of patients with 25(OH)D insufficiency was significantly greater in PMF (48%) and PV (43%) when compared with ET (28%) and MDS (28%) (P = 0.01). Severe 25(OH)D deficiency was significantly more frequent in ET (12%) and PMF (9%), compared with PV (3%) and MDS (1%) (P = 0.05). There were no significant correlations between 25(OH)D insufficiency, or severe deficiency, and a variety of clinical or laboratory variables in PMF, MDS, or PV. Furthermore, Vitamin D insufficiency did not influence either overall or leukemia‐free survival in PMF, MDS, or PV (P > 0.05). We conclude that while hypovitaminosis D is relatively common in MPN and MDS, its clinical relevance for prognosis is limited. © 2011 Wiley‐Liss, Inc.
Pulmonary function testing prior to reduced intensity conditioning allogeneic stem cell transplantation in an unselected patient cohort predicts posttransplantation pulmonary complications and outcome
Authors: Piñana José Luis , Martino Rodrigo , Barba Pere , Bellido‐Casado Jesús , Valcárcel David , Sureda Anna , Briones Javier , Brunet Salut , Rodriguez‐Arias José Manuel , Casan Pere , Sierra Jorge
Published: September 2011

Pretransplant pulmonary function tests (PFTs) have been checked mostly in myeloablative allogeneic stem cell transplantation (Allo‐SCT). Their value in the setting of reduced intensity conditioning Allo‐SCT (Allo‐RIC) has been less explored. We retrospectively evaluated the predictive value of PFTs on posttransplant pulmonary complications (PPC) and outcomes in 195 consecutive Allo‐RIC patients, based on fludarabine plus busulphan or melphalan. PFT parameters included forced vital capacity (FVC), forced expiratory volume in the first second (FEV1), FEV1/FVC ratio, total lung capacity (TLC), residual volume, and diffusion capacity for carbon monoxide (DLCo) corrected for the hemoglobin levels. Pretransplant PFTs abnormalities were observed in 130 patients (66%). The most frequent abnormalities were abnormal DLCO (n = 83, 44%), followed by FEV1/FVC (n = 75, 38%) and FVC (n = 47, 24%). The abnormalities were severe in 25 (13%) patients, moderate in 65 (33%) and mild in 40 patients (21%). Multivariate analysis showed that TLC was significantly associated with PPC, nonrelapse mortality and overall survival (OS), (HR 4.2, 95% CI. 2–8.5; HR 3.8, 95% CI. 1.7–8.5; HR 2.3, 95% CI. 1.3–4.1, respectively, P = 0.01), while abnormal FVC had a negative impact on PPC and OS (HR 1.8, 95% CI. 0.98–3.6, P = 0.06 and HR 1.7, 95% CI. 1.1–2.6, P = 0.008). This study emphasizes the valuable role of PFTs in identifying patients at risk for PPC, NRM, and lower OS in the Allo‐RIC setting. Am. J. Hematol., 2012. © 2011 Wiley Periodicals, Inc.
Synthesis and antimicrobial activity of Schiff base of chitosan and acylated chitosan
Authors: Wang Jiangtao , Lian Ziru , Wang Hedong , Jin Xiaoxiao , Liu Yajuan
Published: September 2011

Chitosan, a biocompatible, biodegradable, nontoxic polymer, is prepared from chitin, which is the second most naturally occurring biopolymer after cellulose. Schiff base of chitosan, sorbyl chitosan, and p‐aminobenzoyl chitosan were synthesized working under high‐intensity ultrasound and their antimicrobial properties were analyzed against Escherichia coli, Staphylococcus aureus, and Aspergillus niger. The structures of the derivatives were characterized by FTIR spectroscopy and elemental analysis. The results of antimicrobial activities indicated that the antimicrobial activities of the derivatives increased with increasing the concentration. The antibacterial activity of schiff base of chitosan against E. coli was stronger, while acylated chitosan had better inhiting effect on S. aureus than others. It was also found that the antifungal activities of the derivatives were stronger than that of chitosan, and schiff base of chitosan was obviously superior to acylated chitosan. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Preparation of hyperbranched epoxy resin containing nitrogen heterocycle and its toughened and reinforced composites
Authors: Chen Sufang , Zhang Daohong , Jiang Shibao , Jia Demin
Published: September 2011

Low‐viscosity hyperbranched epoxy resin‐containing nitrogen heterocycle (HTPE) is synthesized from epichlorohydrin (ECH), dimethylol propionic acid (DMPA), and tris(2‐hydrooxyethyl)‐isocyanurate. The structure and properties of HTPE are characterized by FTIR, GPC, and molecular simulation. The performance of HTPE/diglycidyl ether of bisphenol‐A (DGEBA) composites first increase and then decrease with the increase of the content and molecular weight of HTPE. Compared to those of pure DGEBA, the impact strength, fracture toughness, tensile, and flexural strength of HTPE‐2/DGEBA composite can be enhanced by about 192%, 39%, 18%, and 23%, respectively. The absence of microphase separation and the presence of lots of “protonema” on the fracture surface of the composites are explicated by an in situ reinforcing and toughening mechanism. The intramolecular cavity of HTPE and the strong interaction between HTPE and DGEBA are two key factors to toughening and reinforcing DGEBA. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
The full spectrum of physiological oxygen tensions and step‐changes in oxygen tension affects the neural differentiation of mouse embryonic stem cells
Authors: Mondragon‐Teran Paul , Baboo Jasmin Z. , Mason Chris , Lye Gary J. , Veraitch Farlan S.
Published: September 2011

The beneficial impact of lowering oxygen tension to physiological levels has been demonstrated in a number of stem cell differentiation protocols. The majority of these studies compare normal laboratory oxygen tension with one physiological condition (typically 2–5% O2). In this article, we investigated whether the full spectrum of physiological oxygen tensions (0–20% O2) and step‐changes in oxygen tension could enhance the production of neural populations from of embryonic stem cells (ESCs). We used a model system for the conversion of mouse ESCs into cells expressing one neuroectoderm stem cell marker (nestin) and two neural markers (βIII tubulin and microtubule‐associated protein (MAP2)). 4–10% O2 was associated with large increases in the total production of viable cells and the highest number of cells expressing Nestin, βIII tubulin, and MAP2. However, 4–10% O2 also caused a reduction in the percentage of cells expressing all three markers. Step changes in oxygen tension at the mid‐point of the differentiation process affected the total production of viable cells and the percentage of cells expressing all three markers. We found that the initial oxygen tension and the magnitude of the step‐change were critical variables. A step increase from 0 to 2% O2 mid‐way through the protocol resulted in the highest percentage of cells expressing βIII tubulin (86.5%). In conclusion, we have demonstrated that the full spectrum of physiological oxygen tensions and step changes in oxygen tension represent a powerful tool for the optimisation of neural differentiation processes. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011
Lithium as a Modifier for Morphology and Defect Structure of Porous Magnesium Oxide Materials Prepared by Gel Combustion Synthesis
Authors: Zavyalova Ulyana , Weinberg Gisela , Frandsen Wiebke , Girgsdies Frank , Risse Thomas , Dinse Klaus Peter , Schloegl Robert , Horn Raimund
Published: September 2011

Defect rich MgO nanocrystals arranged in a hierarchic three‐dimensional pore network were synthesized by using gel combustion synthesis (GCS). By adding Li to the combustion precursor, Li‐induced changes in the morphology and defect structure of MgO could be studied systematically. At low Li loadings (up to 1 wt %), the three‐dimensional pore network was resistant to temperatures up to 800 °C, even though the primary MgO nanoparticles had changed their morphology from on average 8 nm size {100} terminated nanocubes to up to 250 nm large complex polyhedral, exposing more and more {111} facets. At higher Li loadings, the primary MgO particles grow even further, to up to 500 nm, causing the three‐dimensional pore network to collapse. After describing the GCS method, detailed structural characterizations of all of the materials synthesized were conducted by means of XRD, BET and pore size analysis, and electron microscopy. IR and thermogravimetric mass spectroscopy (TG‐MS) in combination with XRD were used to investigate the formation and decomposition of carbonate species during synthesis and calcination. Diffuse reflectance UV/Vis (DR‐UV/Vis) spectroscopy was used to characterize surface defects, such as low coordinated O2−ions at edges, corners, and kinks of the MgO surface. Bulk defects were studied by using electron paramagnetic resonance (EPR) spectroscopy. Morphology and defect concentration of the Li/MgO materials were found to be strongly dependent on the fuel‐to‐oxidizer ratio used in the combustion synthesis, the Li concentration, and the calcination atmosphere.
The Absolute Configuration of the Pyrrolosesquiterpenoid Glaciapyrrol A
Authors: Riclea Ramona , Dickschat Jeroen S.
Published: September 2011

The total syntheses of the structurally unique and moderately cytotoxic pyrrolosesquiterpenoid glaciapyrrol A that has been isolated from a marine streptomycete by Macherla et al.1 and of seven of its stereoisomers have been performed from geraniol or nerol, respectively, using a known diastereoselective Ru‐catalysed approach for the synthesis of tetrahydrofurans previously reported by Stark and co‐workers.5 Comparison of 1H and 13C NMR data unambiguously clarified the relative configuration of natural glaciapyrrol A that was previously only partly solved from the available NMR data. An enantioselective synthesis was carried out resulting in the unnatural enantiomer (11S,12R,15R)‐(−)‐glaciapyrrol A. These data establish the absolute configuration of the natural product as (11R,12S,15S)‐(+)‐glaciapyrrol A.
Phosphatidyl myo‐Inositol Mannosides Mimics Built on an Acyclic or Heterocyclic Core: Synthesis and Anti‐inflammatory Properties
Authors: Front Sophie , Court Nathalie , Bourigault Marie‐Laure , Rose Stéphanie , Ryffel Bernhard , Erard François , Quesniaux Valérie F. J. , Martin Olivier R.
Published: September 2011

Phosphatidyl myo‐inositol mannosides (PIMs) are constituents of the mycobacterial cell wall and possess immunomodulatory activities. Certain PIM derivatives have immunoprotective activity and are of interest as anti‐inflammatory agents. In order to identify simplified analogues of PIMs that retain this interesting activity, we have prepared a series of new analogues based either on an acyclic or on a heterocyclic scaffold that replaces the inositol moiety, and evaluated these compounds for their inhibition of LPS‐induced release of NO and pro‐inflammatory cytokines by macrophages. It was found that the inositol moiety can be favourably replaced by an aza‐cyclitol (trihydroxy‐piperidine) or an oxa‐cyclitol (trihydroxy‐tetrahydropyran) unit, and that the configuration of the OH‐carrying carbons does not play a significant role. The biological activity is reduced if the nitrogen atom is free in the aza‐cyclitol unit.
Peculiarities of β‐Pinene Autoxidation
Authors: Neuenschwander Ulrich , Meier Emanuel , Hermans Ive
Published: September 2011

The thermal oxidation of the renewable olefin β‐pinene with molecular oxygen was experimentally and computationally investigated. Peroxyl radicals abstract weakly bonded allylic hydrogen atoms from the substrate, yielding allylic hydroperoxides (i.e., myrtenyl and pinocarvyl hydroperoxide). In addition, peroxyl radicals add to the CC bond of the substrate to form an epoxide. It was found that a relatively high peroxyl radical concentration, together with the high rate of peroxyl cross‐reactions, make radical–radical reactions surprisingly important for this particular substrate. Approximately 60 % of these peroxyl cross‐reactions lead to termination (radical destruction), keeping a radical chain length of approximately 4 at 10 % conversion. Numerical simulation of the reaction—based on the proposed reaction mechanism and known or predicted rate constants—demonstrate the importance of peroxyl cross‐reactions for the formation of alkoxyl radicals, which are the precursor of alcohol and ketone products.
Methylamphetamine synthesis: Does an alteration in synthesis conditions affect the δ13C, δ15N and δ2H stable isotope ratio values of the product?
Authors: Salouros Helen , Collins Michael , Cawley Adam , Longworth Mitchell
Published: September 2011

Conventional chemical profiling of methylamphetamine has long been employed by national forensic laboratories to determine the synthetic route and where possible the precursor chemicals used in its manufacture. This laboratory has been studying the use of stable isotope ratio mass spectrometry (IRMS) analysis as a complementary technique to conventional chemical profiling of fully synthetic illicit drugs such as methylamphetamine. As part of these investigations the stable carbon (δ13C), nitrogen (δ15N), and hydrogen (δ2H) isotope values in the precursor chemicals of ephedrine and pseudoephedrine and the resulting methylamphetamine end‐products have been measured to determine the synthetic origins of methylamphetamine. In this study, results are presented for δ13C, δ15N, and δ2H values in methylamphetamine synthesized from ephedrine and pseudoephedrine by two synthetic routes with varying experimental parameters. It was demonstrated that varying parameters, such as stoichiometry, reaction temperature, reaction time, and reaction pressure, had no effect on the δ13C, δ15N, and δ2H isotope values of the final methylamphetamine product, within measurement uncertainty. Therefore the value of the IRMS technique in identifying the synthetic origin of precursors, such as ephedrine and pseudoephedrine, is not compromised by the potential variation in synthetic method that is expected from one batch to the next, especially in clandestine laboratories where manufacture can occur without stringent quality control of reactions. Copyright © 2011 John Wiley & Sons, Ltd.
Terthiophene Appended with Terpyridine Units as Receptors for Protons and Zn2+ Ions: Photoinduced Energy and Electron Transfer Processes
Authors: Bergamini Giacomo , Boselli Luca , Ceroni Paola , Manca Paola , Sanna Gavino , Pilo Maria
Published: September 2011

Two ligands consisting of 2,2′:6′,2″‐terpyridine (tpy) and terthiophene units (3T) connected by a methyleneoxy (TTT) or an alkynyl bridge (TAT) show different photophysical properties: in the former there is no evidence of a ground state interaction between the two constituent chromophores and the expected 3T emission is observed. On the other hand, the latter exhibits strong π‐conjugation between the two chromophores mediated by the alkynyl bridge: this results in a substantially redshifted absorption and an emission displaced toward the red with a decreased quantum yield. Both of these ligands can be diprotonated: protonation occurs at the tpy unit in two successive steps, leading finally to TTT·2H+ and TAT·2H+. In both cases, strong changes in the absorption spectra and very efficient quenching of the luminescence takes place by a photoinduced electron transfer from 3T to the protonated tpy unit. Both TTT and TAT can also perform as Zn2+ ligands, giving rise to complexes with 1:2 metal/ligand stoichiometry in acetonitrile solution, as demonstrated by changes in the photophysical properties. Also in this case, the resulting complex is not luminescent because of photoinduced electron transfer from 3T to the [Zn(tpy)2]2+ moieties.
Catalytic Oxidative Carbonylation of Arylamines to Ureas with W(CO)6/I2 as Catalyst
Authors: Zhang Li , Darko Ampofo K. , Johns Jennifer I. , McElwee‐White Lisa
Published: September 2011

The oxidative carbonylation of aniline to N,N′‐diphenylurea was carried out by using W(CO)6 as the catalyst, I2 as the oxidant, CO as the carbonyl source and 4‐(dimethylamino)pyridine (DMAP) as base. The reaction conditions were optimized with respect to different bases, molar ratio of DMAP/iodine, temperature, time, and CO pressure. Various p‐substituted arylamines can be converted into the respective symmetrical and unsymmetrical N,N′‐disubstituted ureas in moderate to good yields. The reaction demonstrated broad tolerance of functionality.
Cerebellar oligodendroglial cells have a mesencephalic origin
Authors: Mecklenburg Nora , Garcia‐López Raquel , Puelles Eduardo , Sotelo Constantino , Martinez Salvador
Published: September 2011

While the origin of oligodendroglia in the prosencephalon and spinal cord has been extensively studied and accurately described, the origin of this cell type in the cerebellum is largely unknown. To investigate where cerebellar oligodendrocytes generate and which migratory pathways they follow to reach their final destination in the adult, in ovo transplants were performed using the quail/chick chimeric system. The chimeric embryos were developed up to HH43‐49 (17–19 days of incubation) to map the location of donor cells and analyze their phenotype by immunohistochemistry. As a result, mesencephalic homotopic and homochronic transplants generated cellular migratory streams moving from the grafted epithelium into the host cerebellum, crossing the isthmus mainly through the velum medullare and invading the central white matter. From here, these mesencephalic cells invaded all the layers of the cerebellar cortex except the granular layer. The majority of the cells were detected in the central and folial white matter, as well as in superficial regions of the internal granular layer, surrounding the Purkinje cells. In the latter case, the donor cells presented a Bergmann glial morphology and were Vimentin positive, while in other areas they were PLP and Olig2‐positive, indicating an oligodendroglial fate. The combinatory analysis of the different grafts allowed us to propose the fate map of chick cerebellar oligodendroglia at the neural tube stage. As a result, the majority of the cerebellar oligodendrocytes originate from the parabasal plate of the mesencephalon. © 2011 Wiley‐Liss, Inc.
A gene signature identified using a mouse model of androgen receptor‐dependent prostate cancer predicts biochemical relapse in human disease
Authors: Thompson Vanessa C. , Day Tanya K. , Bianco‐Miotto Tina , Selth Luke A. , Han Guangzhou , Thomas Mervyn , Buchanan Grant , Scher Howard I. , Nelson Colleen C. ,   the Australian Prostate Cancer BioResource, Greenberg Norman M. , Butler Lisa M. , Tilley Wayne D.
Published: September 2011

Mutations in the androgen receptor (AR) have been detected in experimental and clinical prostate tumors. Mice with enforced prostate‐specific expression of one such receptor variant, AR‐E231G, invariably develop prostatic intraepithelial neoplasia by 12 weeks and metastatic prostate cancer by 52 weeks. The aim of this study was to identify genes with altered expression in the prostates of AR‐E231G mice at an early stage of disease that may act as drivers of AR‐mediated tumorigenesis. The gene expression profile of AR‐E231G prostate tissue from 12‐week‐old mice was compared to an equivalent profile from mice expressing the AR‐T857A receptor variant (analogous to the AR‐T877A variant in LNCaP cells), which do not develop prostate tumors. One hundred and thirty‐two genes were differentially expressed in AR‐E231G prostates. Classification of these genes revealed enrichment for cellular pathways known to be involved in prostate cancer, including cell cycle and lipid metabolism. Suppression of two genes upregulated in the AR‐E231G model, ADM and CITED1, increased cell death and reduced proliferation of human prostate cancer cells. Many genes differentially expressed in AR‐E231G prostates are also deregulated in human tumors. Three of these genes, ID4, NR2F1 and PTGDS, which were expressed at consistently lower levels in clinical prostate cancer compared to nonmalignant tissues, formed a signature that predicted biochemical relapse (hazard ratio 2.2, p = 0.038). We believe that our findings support the value of this novel mouse model of prostate cancer to identify candidate therapeutic targets and/or biomarkers of human disease.
Calcium‐regulated transcriptional pathways in the normal and pathologic heart
Authors: Zarain‐Herzberg Angel , Fragoso‐Medina Jorge , Estrada‐Avilés Rafael
Published: September 2011

The cytosolic calcium concentration ([Ca2+]c) is key for the regulation of many cellular processes, such cell signaling and proliferation, metabolism, and muscle contraction. In cardiomyocytes, Ca2+ is an important regulator in many cellular functions such electrophysiological processes, excitation‐contraction coupling, regulation of contractile proteins activity, energy metabolism, cell death, and transcriptional regulation by the activation of Ca2+‐dependent transcriptional pathways. In cardiomyocytes, the two main Ca2+‐dependent pathways are the Ca2+/calmodulin‐calcineurin‐NFAT and the Ca2+/calmodulin‐dependent kinases‐MEF2. Both pathways are involved in the transcriptional control of many cardiac genes. Cardiac hypertrophy (CH) and heart failure (HF) are characterized by alterations in calcium handling such a low sarcoplasmic reticulum Ca2+ content, decreased rate of Ca2+ removal from the sarcoplasm, increased diastolic [Ca2+]c, and decreased systolic [Ca2+]c, all of them contributing to diminished contractibility and force generation in failing heart. At gene expression level, there are also many changes such decreased levels of SERCA2a and activation of a fetal gene expression program in cardiomyocytes. A variety of Ca2+‐dependent signaling pathways have been implicated in CH and HF, but whether these pathways are interrelated and whether there is specificity among them are still unclear and under investigation. The focus of this review is to make an analysis of the current knowledge about the role of Ca2+ signaling pathways in the regulation of cardiac gene expression making special emphasis in novel strategies to correct Ca2+ handling alterations by means of SERCA2a gene therapy. © 2011 IUBMB IUBMB Life, 2011.
Signaling epigenetics: Novel insights on cell signaling and epigenetic regulation
Authors: Arzate‐Mejía Rodrigo G. , Valle‐García David , Recillas‐Targa Félix
Published: September 2011

Cells must be able to respond rapidly and precisely not only to changes in their external environment but also to developmental and differentiation cues to determine when to divide, die, or acquire a particular cell fate. Signal transduction pathways are responsible for the integration and interpretation of most of such signals into specific transcriptional states. Those states are achieved by the modulation of chromatin structure that activates or represses transcription at particular loci. Although a large variety of signal transduction pathways have already been described, much less is known about the crosstalk between signal transduction and its consequent changes in chromatin structure and, therefore, gene expression. Here we present some examples of the relationship between chromatin‐associated proteins and important signal transduction pathways during critical processes like development, differentiation, and disease. There is a great diversity of epigenetic mechanisms that have unexpected interactions with signaling pathways to establish transcriptional programs. Moreover, there are also particular cases where signaling pathways directly affect important components of the epigenetic machinery. Based on such examples, we further propose future research directions linking cell signaling and epigenetics. It is foreseeable that analyzing the relationship between cell signaling and epigenetics will be a huge area for future development that will help us understand the complex process by which a cell is able to induce transcriptional changes in response to external and internal signals. © 2011 IUBMB IUBMB Life, 2011
Molecular control of cell differentiation and programmed cell death during digit development
Authors: Chimal‐Monroy Jesús , Abarca‐Buis René Fernando , Cuervo Rodrigo , Díaz‐Hernández Martha , Bustamante Marcia , Rios‐Flores Jesús Alberto , Romero‐Suárez Silvina , Farrera‐Hernández Alejandro
Published: September 2011

During the hand plate development, the processes of cell differentiation and control of cell death are relevant to ensure a correct shape of the limb. The progenitor cell pool that later will differentiate into cartilage to form the digits arises from undifferentiated mesenchymal cells beneath the apical ectodermal ridge (AER). Once these cells abandon the area of influence of signals from AER and ectoderm, some cells are committed to chondrocyte lineage forming the digital rays. However, if the cells are not committed to chondrocyte lineage, they will form the prospective interdigits that in species with free digits will subsequently die. In this work, we provide the overview of the molecular interactions between different signaling pathways responsible for the formation of digit and interdigit regions. In addition, we briefly describe some experiments concerning the most important signals responsible for promoting cell death. Finally, on the basis that the interdigital tissue has chondrogenic potential, we discuss the hypothesis that apoptotic‐promoting signals might also act as antichondrogenic factors and chondrogenic factors might operate as anti‐apoptotic factors. © 2011 IUBMB IUBMB Life, 2011
Site specificity of OH α‐H abstraction reaction for a β‐hairpin peptide: An ab initio study
Authors: Lin Ren‐Jie , Jang Soonmin , Wu Chen‐Chang , Liu Ya‐Ling , Li Feng‐Yin
Published: September 2011

A β‐hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α‐H atom with ab initio calculation at the B3LYB/6‐31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre‐ and post‐reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α‐H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor‐like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α‐H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α‐H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Timing of Lateglacial vegetation dynamics and respective palaeoenvironmental conditions in southern Estonia: evidence from the sediment record of Lake Nakri
Authors: Amon Leeli , Veski Siim , Heinsalu Atko , Saarse Leili
Published: September 2011

This paper investigates a detailed well‐dated Lateglacial floristic colonisation in the eastern Baltic area, ca. 14 000–9000 cal. a BP, using palynological, macrofossil, loss‐on‐ignition, and 14C data. During 14 000–13 400 cal. a BP, primarily treeless pioneer tundra vegetation existed. Tree birch (Betula sect. Albae) macro‐remains and a high tree pollen accumulation rate indicate the presence of forest‐tundra with birch and possibly pine (Pinus sylvestris L.) trees during 13 400–12 850 cal. a BP. Palaeobotanical data indicate that the colonisation and development of forested areas were very rapid, arising within a period of less than 50 years. Thus far, there are no indications of conifer macrofossils in Estonia to support the presence of coniferous forests in the Lateglacial period. Signs of Greenland Interstadial 1b cooling during 13 100 cal. a BP are distinguishable. Biostratigraphic evidence indicates that the vegetation was again mostly treeless tundra during the final colder episode of the Lateglacial period associated with Greenland Stadial 1, approximately 12 850–11 650 cal. a BP. This was followed by onset of the Holocene vegetation, with the expansion of boreal forests, in response to rapid climatic warming. Copyright © 2011 John Wiley & Sons, Ltd.
Hydrogen Abstraction Followed by Nitroxide‐Mediated Polymerization: Synthesis of 2,7‐Dibromofluorene‐Labeled Polystyrene
Authors: Butcher William E. , Tillman Eric S.
Published: September 2011

Chromophore end‐labeled polystyrene is synthesized using nitroxide‐mediated polymerization (NMP) by decomposing 2‐2′‐azoisobutyronitrile (AIBN) or benzoyl peroxide (BPO) in the presence of fluorene or fluorene derivatives. End‐labeling is dependent on the thermally produced radical species selectively abstracting a hydrogen atom from the 9‐position of the fluorene species prior to initiation of styrene. From gel permeation chromatography (GPC) data and UV–Vis analysis, it is found that AIBN initiation, compared to BPO, leads to a more controlled polymerization system, producing polymers with predictable molecular weights, narrower polydispersity index (PDI) values (<1.3), and higher amounts of fluorene end‐labeling. In terms of the reaction parameters, no consistent trend is observed as a function of the timing of styrene's addition or the temperature at which the hydrogen abstraction phase is performed. Analysis of the chromophore content by UV–Vis spectroscopy demonstrated that the presence of bromine atoms on the 2‐ and 7‐position of the fluorene species leads to higher percent labeling of the chromophore species, presumably due to a more facile abstraction of the hydrogen at the 9‐position.
Global attractor for a three‐species predator‐prey model with cross‐diffusion
Authors: Guo Haojie , Zheng Sining
Published: September 2011

This paper studies a three‐species predator‐prey model with cross‐diffusion. In a previous paper 11 of Pang and Wang, it was proved that the system admits global classical solutions if the exponents in cross diffusion term satisfy m, l ≥ 1. In the present paper, we continue considering the asymptotic behavior of the solutions, and obtain that the system possesses a global attractor in fact, if the cross diffusion exponents are even larger with m, l ≥ 2.