bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Aptamers and Spiegelmers: Synthesis, Purification, and Post‐Synthetic PEG Conjugation
Authors: Hoffmann Stefanie , Hoos Johannes , Klussmann Sven , Vonhoff Stefan 
Published: September 2011

AbstractThis 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

AbstractOrthoMCL 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

AbstractThe 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

AbstractThis 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

AbstractThe 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

AbstractVitamin 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

AbstractPretransplant 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

AbstractChitosan, 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

AbstractLow‐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

AbstractThe 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

AbstractDefect 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

AbstractThe 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

AbstractPhosphatidyl 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

AbstractThe 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.
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

AbstractTwo 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

AbstractThe 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

AbstractWhile 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.