bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bio‐organic reaction animations (BioORA): Student performance, student perceptions, and instructor feedback
Authors: Gunersel Adalet Baris , Fleming Steven 
Published: February 2014

AbstractResearch shows that computer animations are especially helpful in fields such as chemistry and in this mixed‐methods study, we investigate the educational effectiveness of Bio‐Organic Reaction Animations (BioORA), a 3‐D software, in four undergraduate biochemistry classes at different universities. Statistically significant findings indicate that students performed better on a quiz completed after a lesson with BioORA than after a lesson with regular teaching methods in three out of four classes. Ratings on several survey items completed after experiencing BioORA, including items related to interest, value, and ability, were higher in two classes. Surveys and one‐on‐one interviews reveal instructor and student experiences with the software as well as the utility of various software features, which can be adopted in other programs. Instructors and students provide suggestions to maximize BioORA's benefits as an educational tool and findings suggest the importance of multiple forms of information to enhance student understanding and reach students with various learning preferences. © 2014 by The International Union of Biochemistry and Molecular Biology, 42(3):XXXXX–XXXXX, 2014.
Modulation of circulating protein biomarkers following TRC105 (anti‐endoglin antibody) treatment in patients with advanced cancer
Authors: Liu Yingmiao , Starr Mark D. , Brady John C. , Dellinger Andrew , Pang Herbert , Adams Bonne , Theuer Charles P. , Lee Nam Y. , Hurwitz Herbert I. , Nixon Andrew B. 
Published: February 2014

AbstractTRC105 is an endoglin‐targeting drug that possesses anti‐angiogenic and antitumor potential. Analysis of the initial phase I trial of TRC105 demonstrated good tolerability and efficacy in cancer patients. In this report, we analyzed multiple circulating biomarkers at baseline, cycle 2 day 1 (C2D1), and end of study (EOS) for each patient. The baseline level and the fold change from baseline to both C2D1 and EOS for each marker were statistically analyzed. At C2D1, seven markers were significantly downregulated (angiopoietin‐2 [Ang‐2], insulin‐like growth factor‐binding protein‐3 [IGFBP‐3], plasminogen activator inhibitor‐1 [PAI‐1] total, platelet‐derived growth factor [PDGF]‐AA, PDGF‐BB, thrombospondin‐1 [TSP‐1], and vascular endothelial growth factor [VEGF]‐D). Meanwhile, seven markers were upregulated by C2D1 (E‐Cadherin, soluble Endoglin [sEnd], E‐Selectin, interleukin‐6 [IL‐6], osteopontin [OPN], TSP‐2, and von Willebrand factor [vWF]). At EOS, seven markers were upregulated including Ang‐2, C‐reactive protein (CRP), intercellular adhesion molecule‐1 (ICAM‐1), IGFBP‐1, IL‐6, TSP‐2, and vascular cell adhesion molecule‐1 (VCAM‐1). A statistical trend was also seen for increases of VEGF‐A and placenta growth factor (PlGF) at EOS. Throughout treatment, sEnd levels significantly increased, an observation that was recapitulated in cultured endothelial cells. This is the first report of plasma‐based biomarkers in patients receiving TRC105. TRC105 treatment by C2D1 was associated with decreases in several angiogenic factors, including Ang‐2, PDGF isoforms, and VEGF isoforms, offering insight into the mechanisms underlying TRC105's anti‐angiogenic, antitumor function. Increases in sEnd were the most significant of all observed biomarker changes and may reflect direct drug effects. Additionally, biomarker changes in response to TRC105 are distinct from those seen in patients treated with VEGF‐targeting drugs, suggesting the possible utility of combining these two classes of angiogenesis inhibitors in patients.
Response assessment of NovoTTF‐100A versus best physician's choice chemotherapy in recurrent glioblastoma
Authors: Wong Eric T. , Lok Edwin , Swanson Kenneth D. , Gautam Shiva , Engelhard Herbert H. , Lieberman Frank , Taillibert Sophie , Ram Zvi , Villano John L. 
Published: February 2014

AbstractThe NovoTTF‐100A device emits frequency‐tuned alternating electric fields that interfere with tumor cell mitosis. In phase III trial for recurrent glioblastomas, NovoTTF‐100A was shown to have equivalent efficacy and less toxicity when compared to Best Physician's Choice (BPC) chemotherapy. We analyzed the characteristics of responders and nonresponders in both cohorts to determine the characteristics of response and potential predictive factors. Tumor response and progression were determined by Macdonald criteria. Time to response, response duration, progression‐free survival (PFS) ± Simon–Makuch correction, overall survival (OS), prognostic factors, and relative hazard rates were compared between responders and nonresponders. Median response duration was 7.3 versus 5.6 months for NovoTTF‐100A and BPC chemotherapy, respectively (P = 0.0009). Five of 14 NovoTTF‐100A responders but none of seven BPC responders had prior low‐grade histology. Mean cumulative dexamethasone dose was 35.9 mg for responders versus 485.6 mg for nonresponders in the NovoTTF‐100A cohort (P < 0.0001). Hazard analysis showed delayed tumor progression in responders compared to nonresponders. Simon–Makuch‐adjusted PFS was longer in responders than in nonresponders treated with NovoTTF‐100A (P = 0.0007) or BPC chemotherapy (P = 0.0222). Median OS was longer for responders than nonresponders treated with NovoTTF‐100A (P < 0.0001) and BPC chemotherapy (P = 0.0235). Pearson analysis showed strong correlation between response and OS in NovoTTF‐100A (P = 0.0002) but not in BPC cohort (P = 0.2900). Our results indicate that the response characteristics favor NovoTTF‐100A and data on prior low‐grade histology and dexamethasone suggest potential genetic and epigenetic determinants of NovoTTF‐100A response.
Development of Selective Inhibitors for Human Aldehyde Dehydrogenase 3A1 (ALDH3A1) for the Enhancement of Cyclophosphamide Cytotoxicity
Authors: Parajuli Bibek , Georgiadis Taxiarchis M. , Fishel Melissa L. , Hurley Thomas D. 
Published: February 2014

AbstractAldehyde dehydrogenase 3A1 (ALDH3A1) plays an important role in many cellular oxidative processes, including cancer chemoresistance, by metabolizing activated forms of oxazaphosphorine drugs such as cyclophosphamide (CP) and its analogues, such as mafosfamide (MF), ifosfamide (IFM), and 4‐hydroperoxycyclophosphamide (4‐HPCP). Compounds that can selectively target ALDH3A1 could permit delineation of its roles in these processes and could restore chemosensitivity in cancer cells that express this isoenzyme. Here we report the detailed kinetic and structural characterization of an ALDH3A1‐selective inhibitor, CB29, previously identified in a high‐throughput screen. Kinetic and crystallographic studies demonstrate that CB29 binds within the aldehyde substrate‐binding site of ALDH3A1. Cellular proliferation of ALDH3A1‐expressing lung adenocarcinoma (A549) and glioblastoma (SF767) cell lines, as well as ALDH3A1 non‐expressing lung fibroblast (CCD‐13Lu) cells, is unaffected by treatment with CB29 and its analogues alone. However, sensitivity toward the anti‐proliferative effects of mafosfamide is enhanced by treatment with CB29 and its analogue in the tumor cells. In contrast, the sensitivity of CCD‐13Lu cells toward mafosfamide was unaffected by the addition of these same compounds. CB29 is chemically distinct from the previously reported small‐molecule inhibitors of ALDH isoenzymes and does not inhibit ALDH1A1, ALDH1A2, ALDH1A3, ALDH1B1, or ALDH2 isoenzymes at concentrations up to 250 μM. Thus, CB29 is a novel small molecule inhibitor of ALDH3A1, which might be useful as a chemical tool to delineate the role of ALDH3A1 in numerous metabolic pathways, including sensitizing ALDH3A1‐positive cancer cells to oxazaphosphorines.
Anticancer Potency Studies of Coordination Driven Self‐Assembled Arene–Ru‐Based Metalla‐Bowls
Authors: Mishra Anurag , Jeong Yong Joon , Jo Jae‐Ho , Kang Se Chan , Lah Myoung Soo , Chi Ki‐Whan 
Published: February 2014

AbstractNew tetranuclear cationic metalla‐bowls5–7with the general formula [Ru4(p‐cymene)4(N∩N)2(OO∩OO)2]4+(N∩N=2,6‐bis(N‐(4‐pyridyl carbamoyl)pyridine, OO∩OO=2,5‐dihydroxy‐1,4‐benzoquinonato (5), OO∩OO=5,8‐dioxydo‐1,4‐naphthaquinonato (6), OO∩OO=hoxonato (7)) were prepared by the reaction of the respective dinuclear ruthenium complexes2–4with a bispyridine amide donor ligand1in methanol in the presence of AgO3SCF3.These new molecular metalla‐bowls were fully characterized by analytical techniques including elemental analysis as well as1H and13C NMR and HR‐ESI‐MS spectroscopy. The structure of metalla‐bowl6was determined from X‐ray crystal diffraction data. A UV/visible study was also carried out for the entire suite of new complexes. As with recent studies of similar arene–Ru complexes, the inhibition of cell growth by metalla‐bowls was established against SK‐hep‐1 (liver cancer), AGS (gastric cancer), and HCT‐15 (colorectal cancer) human cancer cell lines. Inhibition of cell growth by6was found to be considerably stronger against all cancer cell lines than the anticancer drugs, doxorubicin and cisplatin. In particular, in colorectal cancer cells, expression of the cancer suppressor genes APC and p53 was increased following exposure to6.
Targeted Mutagenesis Results in an Activation of DNA Methyltransferase 1 and Confirms an Autoinhibitory Role of its RFTS Domain
Authors: Bashtrykov Pavel , Rajavelu Arumugam , Hackner Benjamin , Ragozin Sergey , Carell Thomas , Jeltsch Albert 
Published: February 2014

AbstractThe N‐terminal regulatory part of DNA methyltransferase 1 (Dnmt1) contains a replication foci targeting sequence (RFTS) domain, which is involved in the recruitment of Dnmt1 to replication forks. The RFTS domain has been observed in a crystal structure to bind to the catalytic domain of the enzyme and block its catalytic centre. Removal of the RFTS domain led to activation of Dnmt1, thus suggesting an autoinhibitory role of this domain. Here, we destabilised the interaction of the RFTS domain with the catalytic domain by site‐directed mutagenesis and purified the corresponding Dnmt1 variants. Our data show that these mutations resulted in an up to fourfold increase in Dnmt1 methylation activity in vitro. Activation of Dnmt1 was not accompanied by a change in its preference for methylation of hemimethylated CpG sites. We also show that the Dnmt1 E572R/D575R variant has a higher DNA methylation activity in human cells after transfection into HCT116 cells, which are hypomorphic for Dnmt1. Our findings strongly support the autoinhibitory role of the RFTS domain, and indicate that it contributes to the regulation of Dnmt1 activity in cells.
Functional Characterization of E. coli LptC: Interaction with LPS and a Synthetic Ligand
Authors: Sestito Stefania E. , Sperandeo Paola , Santambrogio Carlo , Ciaramelli Carlotta , Calabrese Valentina , Rovati G. Enrico , Zambelloni Luca , Grandori Rita , Polissi Alessandra , Peri Francesco 
Published: February 2014

AbstractLipopolysaccharide (LPS), the main cell‐surface molecular constituent of Gram‐negative bacteria, is synthesized in the inner membrane (IM) and transported to the outer membrane (OM) by the Lpt (lipopolysaccharide transport) machinery. Neosynthesized LPS is first flipped by MsbA across the IM, then transported to the OM by seven Lpt proteins located in the IM (LptBCFG), in the periplasm (LptA), and in the OM (LptDE). A functional OM is essential to bacterial viability and requires correct placement of LPS in the outer leaflet. Therefore, LPS biogenesis represents an ideal target for the development of novel antibiotics against Gram‐negative bacteria. Although the structures of Lpt proteins have been elucidated, little is known about the mechanism of LPS transport, and few data are available on Lpt–LPS binding. We report here the first determination of the thermodynamic and kinetic parameters of the interaction between LptC and a fluorescent lipo‐oligosaccharide (fLOS) in vitro. The apparent dissociation constant (Kd) of the fLOS–LptC interaction was evaluated by two independent methods. The first was based on fLOS capture by resin‐immobilized LptC; the second used quenching of LptC intrinsic fluorescence by fLOS in solution. The Kd values by the two methods (71.4 and 28.8 μm, respectively) are very similar, and are of the same order of magnitude as that of the affinity of LOS for the upstream transporter, MsbA. Interestingly, both methods showed that fLOS binding to LptC is mostly irreversible, thus reflecting the fact that LPS can be released from LptC only when energy is supplied by ATP or in the presence of a higher‐affinity LptA protein. A fluorescent glycolipid was synthesized: this also interacted irreversibly with LptC, but with lower affinity (apparent Kd=221 μM). This compound binds LptC at the LPS binding site and is a prototype for the development of new antibiotics targeting LPS transport in Gram‐negative bacteria.
The Amplatzer duct occluder II additional sizes device for transcatheter PDA closure: Initial experience
Authors: Bruckheimer Elchanan , Godfrey Max , Dagan Tamir , Levinzon Michael , Amir Gabriel , Birk Einat 
Published: February 2014

ObjectivesTo present our initial experience with the Amplatzer Duct Occluder II Additional Sizes (ADOIIAS) device.BackgroundThe ADOIIAS is a modified PDA closure device of various lengths and widths with small disks to avoid flow disturbance in the pulmonary arteries and descending aorta.MethodsPatient population: All patients who underwent attempted closure with an ADOIIAS device at our institutionCatheterizationFollowing aortography the PDA was closed using a 4–5Fr delivery system from the pulmonary or aortic side with an ADOIIAS. Aortography to confirm position and leak was performed before and after device release. Echocardiography was performed before discharge the following day.ResultsBetween June 2011 and December 2012, 60 patients [33 female], median age 3.3 yrs [0.6–15.8 years], and weight 14.5 kg [4–79] underwent attempted PDA closure with an ADOIIAS device. 56/60 [93.3%] ADOIIAS devices were successfully deployed [52 aortic side]. In 55/56 [98.2%], the PDA was closed on follow up echocardiogram usually on the next day. In one case, there was a small residual PDA of no hemodynamic significance on follow up. In four cases, the ADOIIAS was unstable, including one device embolization which was retrieved with no sequelae, and the PDA was closed in all cases with an alternative device in the same procedure. The mean ratio of ADOIIAS height:PDA pulmonary diameter was 2.4 ± 0.5:1.ConclusionsWe report a large single‐center experience with the new ADOIIAS device which proved to be versatile, safe, effective, and easy to use in the appropriate ductal anatomy. © 2014 Wiley Periodicals, Inc.
Rhodium‐Complex‐Linked Hybrid Biocatalyst: Stereo‐Controlled Phenylacetylene Polymerization within an Engineered Protein Cavity
Authors: Fukumoto Kazuki , Onoda Akira , Mizohata Eiichi , Bocola Marco , Inoue Tsuyoshi , Schwaneberg Ulrich , Hayashi Takashi 
Published: February 2014

AbstractThe incorporation of a Rh complex with a maleimide moiety into the cavity of the nitrobindin β‐barrel scaffold by a covalent linkage at the 96‐position (Cys) provides a hybrid biocatalyst that promotes the polymerization of phenylacetylene. The appropriate structural optimization of the cavity by mutagenesis enhances the stereoselectivity of the polymer with a trans content of 82 % at 25 °C and pH 8.0. The X‐ray crystal structure of one of the hybrid biocatalysts at a resolution of 2.0 Å reveals that the Rh complex is located in the β‐barrel cavity without any perturbation to the total protein structure. Crystal structure analysis and molecular modeling support the fact that the stereoselectivity is enhanced by the effective control of monomer access to the Rh complex within the limited space of the protein cavity.
Regioselective Enzymatic Halogenation of Substituted Tryptophan Derivatives using the FAD‐Dependent Halogenase RebH
Authors: Frese Marcel , Guzowska Paulina H. , Voß Hauke , Sewald Norbert 
Published: February 2014

AbstractRegioselective methods to establish carbon–halide bonds are still rare, although halogenation is considered as a commonly used methodology for the functionalization of organic compounds. The incorporation of halogen substituents by organic synthesis usually requires hazardous conditions, shows poor regioselectivity and results in the formation of unwanted byproducts. In addition, halogenation by electrophilic aromatic substitution (SEAr) obeys distinct rules depending on electron‐withdrawing or ‐donating groups already present in the aromatic ring. We employed the tryptophan‐7‐halogenase RebH for regioselective enzymatic halogenation to overcome these limitations. In combination with a tryptophan synthase, an array of C5‐ and C6‐substituted tryptophan derivatives was synthesized and halogenated by RebH. The halogenase is able override these directing effects and halogenates at the electronically unfavored C7‐meta‐position, even in presence of ortho/para‐directing groups.
Color Polymorphism: Understanding the Diverse Solid‐State Packing and Color in Dimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate
Authors: Pratik Saied Md. , Nijamudheen Abdulrahiman , Bhattacharya Sumantra , Datta Ayan 
Published: February 2014

AbstractDimethyl‐3,6‐dichloro‐2,5‐dihydroxyterephthalate (MCHT) is known to exist in three differently packed crystals having three different colors, namely yellow (Y), light yellow (LY), and white (W). Apart from the difference in their color, the molecules in the crystals also differ in their intramolecular OH⋅⋅⋅O and OH⋅⋅⋅Cl hydrogen bonds. Time‐dependent DFT calculations reveal the role of the various types of hydrogen bonds in controlling the color of the polymorphs. Mechanistic pathways that lead to such transformations in the crystal are elucidated by solid‐state dispersion‐corrected DFT studies. Relative stabilities of the various polymorphs rationalize the experimentally observed transformations between them. Calculations reveal that the minimum‐energy pathway for the conversion of the Y form to a W form is through stepwise disrotatory motion of the two OH groups through a hybrid intermediate having one intramolecular OH⋅⋅⋅O and one OH⋅⋅⋅Cl bond. The LY form is shown to exist on the higher‐energy pathway involving a concerted Y→W transformation.
Characterization of Supramolecular Hidden Chirality of Hydrogen‐Bonded Networks by Advanced Graph Set Analysis
Authors: Sasaki Toshiyuki , Ida Yoko , Hisaki Ichiro , Yuge Tetsuharu , Uchida Yoshiaki , Tohnai Norimitsu , Miyata Mikiji 
Published: February 2014

AbstractSupramolecular hidden chirality of hydrogen‐bonded (HB) networks of primary ammonium carboxylates was exposed by advanced graph set analysis from a symmetric viewpoint in topology. The ring‐type HB (R‐HB) networks are topologically regarded as faces, and therefore exhibit prochirality and positional isomerism due to substituents attached on the faces. To describe the symmetric properties of the faces, additional symbols, Re (right‐handed or clockwise), Si (left‐handed or anticlockwise), and m (mirror), were proposed. According to the symbols, various kinds of faces were classified based on the symmetry. This symmetry consideration of the faces enables us to precisely evaluate supramolecular chirality, especially its handedness, of 0D‐cubic, 1D‐ladder and 2D‐sheet HB networks that are composed of the faces. The 1D‐ladder and 2D‐sheet HB networks generate chirality by accumulating the chiral faces in 1D and 2D manners, respectively, whereas 0D‐cubic HB networks generate chirality based on combinations of eight kinds of faces, similar to the chirality of dice.
Gold/Acid‐Co‐catalyzed Direct Microwave‐Assisted Synthesis of Fused Azaheterocycles from Propargylic Hydroperoxides
Authors: Alcaide Benito , Almendros Pedro , Quirós M. Teresa 
Published: February 2014

AbstractThe gold–acid‐co‐catalyzed synthesis of nine series of fused azaheterocycles with structural diversity starting from the same synthons as readily available propargylic hydroperoxides and aromatic amines has been achieved. The overall tandem process consists in a gold‐catalyzed hydroperoxide rearrangement/Michael reaction followed by a final acid‐catalyzed cyclization.
Surface‐Junction Effects on Interfacial Electron Transfer between Bis(terpyridine)iron(II) and Hydrogen‐Terminated Silicon(111) Electrode
Authors: Maeda Hiroaki , Sakamoto Ryota , Nishihara Hiroshi 
Published: February 2014

AbstractInterfacial electron transfer at bis(tpy)–iron(II) complexes (tpy=2,2′:6′,2′′‐terpyridine) on Si(111) electrodes was investigated by using four types of surface‐anchor terpyridine ligands. Despite the greater distance, electron transfer between the bis(tpy)–iron(II) unit and the electrode is accelerated in surface‐anchor ligands with an additional phenylene group.
Mixed‐Ligand Catalysts: A Powerful Tool in Transition‐Metal‐Catalyzed Cross‐Coupling Reactions
Authors: Fan Yuting , Cong Mei , Peng Ling 
Published: February 2014

AbstractTransition‐metal‐catalyzed cross‐coupling reactions have fundamentally revolutionized organic synthesis, empowering the otherwise difficult to achieve products with rapid and convenient accesses alongside excellent yields. Within these reactions, ligands often play a critical role in specifically and effectively advocating the corresponding catalysis. Consequently, a myriad of ligands have been created and applied to make a fine tuning of electronic and steric effect of catalysts, remarkably promoting catalytic efficiency and applicability. The “mixed‐ligand” concept has recently emerged; by combining and capitalizing on the superiority of each individual ligand already available, an expedient way can be achieved to reach a larger extent of catalytic diversity and efficacy. Given the availability of a wealth of ligands, it is reasonable to have great expectations for the original application of mixed‐ligand catalytic systems and their important value in organic synthesis.
Carbene‐9‐BBN Ring Expansions as a Route to Intramolecular Frustrated Lewis Pairs for CO2 Reduction
Authors: Wang Tongen , Stephan Douglas W. 
Published: February 2014

AbstractReactions of phosphine‐derived carbenes with 9‐borabicyclo[3.3.1]nonane (9‐BBN) result in ring‐expansion reactions to generate novel intramolecular frustrated Lewis pairs (FLPs). These FLPs effect the catalytic reduction of CO2 in the presence of boranes to give BOB and methoxy‐borate species.
ChemInform Abstract: MYb(BH4)4 (M: K, Na) from Laboratory X‐Ray Powder Data.
Authors: Wegner Wojciech , Jaron Tomasz , Grochala Wojciech 
Published: February 2014

AbstractPolycrystalline KYb(BH4)4 and NaYb(BH4)4 are prepared by solid state mechanochemical reactions of 1:3:1 mixtures of YbCl3, LiBH4, and KBH4 or NaBH4, resp.
ChemInform Abstract: Crystal Structures of Hydrates of Simple Inorganic Salts. Part 1. Water‐Rich Magnesium Halide Hydrates MgCl2·8H2O, MgCl2·12H2O, MgBr2·6H2O, MgBr2·9H2O, MgI2·8H2O and MgI2·9H2O.
Authors: Hennings Erik , Schmidt Horst , Voigt Wolfgang 
Published: February 2014

AbstractCrystals of MgCl2·8H2O (I), MgCl2·12H2O (II), MgBr2·6H2O (III), MgBr2·9H2O (IV), MgI2·8H2O (V), and MgI2·9H2O (VI) are grown from their aqueous solutions at below 298 K according to their solid‐liquid phase diagrams.
ChemInform Abstract: The Double Molybdate Na9Sc(MoO4)6 Refined from Powder XRD Data.
Authors: Savina Aleksandra A. , Morozov Vladimir A. , Basovich Olga M. , Khaikina Elena G. , Lazoryak Bogdan I. 
Published: February 2014

AbstractNa9Sc(MoO4)6 is prepared by solid state reaction of a stoichiometric mixture of Na2MoO4 and Sc2(MoO4)3 (air, 773→873 K in steps of 50 K, 24 h per step).
ChemInform Abstract: Characterization of Solid Acid Electrolyte CsH5(PO4)2 by NMR Spectroscopy.
Authors: Chae Seen Ae , Lee Young Eun , Han Oc Hee , Kim Dong Hoon , Lee Hong‐In 
Published: February 2014

AbstractThe pure title compound (obtained from aqueous slurries of H3PO4 and Cs2CO3 at 100 °C for 24 h) is characterized by 1H, 31P, and 133Cs MAS NMR spectroscopy.